Process merged multiome objects
Libraries
library(tidyr)
library(dplyr)
library(ggplot2)
library(purrr)
library(readr)
library(viridis)
library(Seurat)
library(Signac)
library(Azimuth)
library(EnsDb.Hsapiens.v86)
library(BSgenome.Hsapiens.UCSC.hg38)
library(GenomicRanges)
library(harmony)
library(pheatmap)
library(data.table)
set.seed(1234)
options(repr.matrix.max.cols=100, repr.matrix.max.rows=50)
options(warn=-1)
source("../../../functions_r/scRNAseq.R")
ggplot2::theme_set(theme_min())Set up object
brain_region <- 'Hippocampus'
data_dir = paste0('/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/03-integration/merged_objects/')
integrated_object_path = paste0(data_dir, brain_region, '.merged.multiome.rds')
metadata_all_path = '/oak/stanford/groups/akundaje/projects/psychencode/outs/7_26_2023_multiome_analysis/metadata/multiome.qc.tsv'
integrated_object_path## [1] "/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/03-integration/merged_objects/Hippocampus.merged.multiome.rds"obj <- readRDS(integrated_object_path)
obj## An object of class Seurat
## 354835 features across 137679 samples within 2 assays
## Active assay: RNA (36601 features, 0 variable features)
## 2 layers present: counts, data
## 1 other assay present: ATACVersion(obj)## [1] '5.0.0'# add 'sample' column
obj@meta.data$sample <- obj@meta.data$orig.ident
head(obj@meta.data)## orig.ident nCount_RNA
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 1156-Control-Hippocampus 145402
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 1156-Control-Hippocampus 139613
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 1156-Control-Hippocampus 134099
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 1156-Control-Hippocampus 127166
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 1156-Control-Hippocampus 121561
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 1156-Control-Hippocampus 115519
## nFeature_RNA barcode
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 10646 CAAACCGTCTGTTCAT-1
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 10253 AGTACGCGTTTGGCGG-1
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 10251 GGATTTATCCTCGATC-1
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 10544 CGTAACCCAAGCTAAA-1
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 9714 ATGTAACGTCTTGCTG-1
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 10540 CATCCTGGTATTGGAT-1
## gex_barcode
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 CAAACCGTCTGTTCAT-1
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 AGTACGCGTTTGGCGG-1
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 GGATTTATCCTCGATC-1
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 CGTAACCCAAGCTAAA-1
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 ATGTAACGTCTTGCTG-1
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 CATCCTGGTATTGGAT-1
## atac_barcode is_cell
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 GGCTAATAGTTAGTAG-1 1
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 CCTGGTCCACATGCTT-1 1
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 CAGTGTGAGAACCTGG-1 1
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 AGCTTGTGTAATCGCT-1 1
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 GAAGGTGCATGGATAT-1 1
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 AACCGCGCATTACTGC-1 1
## excluded_reason gex_raw_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0 343330
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0 318177
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0 327874
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0 297819
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0 266038
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0 295263
## gex_mapped_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 329771
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 305565
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 315601
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 285747
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 255061
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 283993
## gex_conf_intergenic_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 27732
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 25282
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 23446
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 25110
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 22349
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 24129
## gex_conf_exonic_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 37587
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 36708
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 34621
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 35467
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 29635
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 36983
## gex_conf_intronic_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 250122
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 230991
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 245826
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 213166
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 191574
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 211530
## gex_conf_exonic_unique_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 33186
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 32906
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 29898
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 31995
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 26800
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 31843
## gex_conf_exonic_antisense_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 4119
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 3534
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 4478
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 3259
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 2639
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 4880
## gex_conf_exonic_dup_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 13535
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 13200
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 12266
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 12805
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 10105
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 13059
## gex_exonic_umis
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 19178
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 19209
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 17207
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 18683
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 16272
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 18338
## gex_conf_intronic_unique_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 221898
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 207306
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 211042
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 190491
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 174349
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 174580
## gex_conf_intronic_antisense_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 23916
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 19321
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 30837
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 19009
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 13847
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 33714
## gex_conf_intronic_dup_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 92875
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 83865
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 91480
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 79442
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 66730
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 75142
## gex_intronic_umis
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 126253
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 120439
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 116918
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 108499
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 105323
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 97214
## gex_conf_txomic_unique_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 31216
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 30813
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 28008
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 30081
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 25370
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 30070
## gex_umis_count gex_genes_count
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0 0
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0 0
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0 0
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0 0
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0 0
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0 0
## atac_raw_reads atac_unmapped_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 43360 254
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 11995 70
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 51227 276
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 69610 388
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 20392 98
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 76448 346
## atac_lowmapq atac_dup_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 2967 13501
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 1226 3503
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 3209 16879
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 4598 23065
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 1848 6951
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 5046 25534
## atac_chimeric_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 48
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 21
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 43
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 83
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 27
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 74
## atac_mitochondrial_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 171
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 2
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 49
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 318
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 79
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 320
## atac_fragments atac_TSS_fragments
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 26410 4703
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 7150 957
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 30758 5640
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 41119 7474
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 11352 1772
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 45094 8692
## atac_peak_region_fragments
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 4471
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 817
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 5226
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 6110
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 1499
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 8677
## atac_peak_region_cutsites
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 7931
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 1452
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 9198
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 10691
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 2649
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 15378
## nCount_ATAC nFeature_ATAC
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 10784 9788
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 2188 2138
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 13201 11890
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 14935 12864
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 3920 3753
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 20516 17489
## nucleosome_signal
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 1.6092156
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0.9012915
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 1.5591801
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 1.3148219
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 1.0151515
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 1.3918440
## nucleosome_percentile
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0.98
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0.70
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0.98
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0.93
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0.80
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0.95
## TSS.enrichment TSS.percentile
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 3.102337 0.47
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 2.268102 0.35
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 2.617383 0.39
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 2.983224 0.44
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 2.405214 0.37
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 2.971033 0.44
## pct_frags_in_peaks percent.mt
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 16.92919 0.4711077
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 11.42657 0.0250693
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 16.99070 0.1603293
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 14.85931 0.1981662
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 13.20472 0.1785112
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 19.24203 0.6665570
## nCount_SCT nFeature_SCT
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 5105 2608
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 5441 2518
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 5090 2578
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 6430 2990
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 5327 2319
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 5339 2883
## nCount_refAssay nFeature_refAssay
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 145402 10646
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 139613 10253
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 134099 10251
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 127166 10544
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 121561 9714
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 115519 10540
## predicted.class.score
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 1
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 1
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 1
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 1
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 1
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 1
## predicted.class
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 Glutamatergic
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 Glutamatergic
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 Glutamatergic
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 GABAergic
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 Glutamatergic
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 Glutamatergic
## predicted.cluster.score
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0.2749085
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0.2927073
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0.3032498
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0.5728458
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0.2601393
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0.2714480
## predicted.cluster
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 Exc L2 LAMP5 KCNG3
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 Exc L2 LAMP5 KCNG3
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 Exc L2 LAMP5 KCNG3
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 Inh L1-3 SST FAM20A
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 Exc L2 LAMP5 KCNG3
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 Exc L2 LAMP5 KCNG3
## predicted.subclass.score
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0.5874844
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0.5648823
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0.6244408
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0.8180437
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0.5697701
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0.5908260
## predicted.subclass
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 L2/3 IT
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 L2/3 IT
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 L2/3 IT
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 Sst
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 L2/3 IT
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 L2/3 IT
## predicted.cross_species_cluster.score
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0.5874844
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0.5648823
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0.6244408
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0.7974378
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0.5697701
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0.5908260
## predicted.cross_species_cluster
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 L2/3 IT
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 L2/3 IT
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 L2/3 IT
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 Sst_3
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 L2/3 IT
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 L2/3 IT
## mapping.score SCT_snn_res.0.8
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0.4803418 14
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0.6165295 14
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0.4102896 14
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0.9942214 10
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0.6244192 14
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0.4495509 14
## seurat_clusters atac_doublets
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 14 singlet
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 14 singlet
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 14 singlet
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 10 singlet
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 14 singlet
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 14 singlet
## pANN_0.25_0.01_35
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0.2758621
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0.2413793
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0.2068966
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0.2413793
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0.2413793
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0.2413793
## DF.classifications_0.25_0.01_35
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 Singlet
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 Singlet
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 Singlet
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 Singlet
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 Singlet
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 Singlet
## rna_doublets all_doublets
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 singlet singlet
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 singlet singlet
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 singlet singlet
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 singlet singlet
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 singlet singlet
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 singlet singlet
## region pANN_0.25_0.01_293
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 Hippocampus NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 Hippocampus NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 Hippocampus NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 Hippocampus NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 Hippocampus NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 Hippocampus NA
## DF.classifications_0.25_0.01_293
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_215
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_215
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_295
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_295
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_410
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_410
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_122
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_122
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_289
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_289
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_141
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_141
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_134
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_134
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_30
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_30
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_64
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_64
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_199
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_199
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_283
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_283
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_203
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_203
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_272
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_272
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_652
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_652
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_268
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_268
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_182
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_182
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_36
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_36
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_65
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_65
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_71
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_71
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_117
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_117
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_408
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_408
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_285
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_285
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_113
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_113
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_379
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_379
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_201
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_201
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_138
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_138
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## sample
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 1156-Control-Hippocampus
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 1156-Control-Hippocampus
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 1156-Control-Hippocampus
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 1156-Control-Hippocampus
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 1156-Control-Hippocampus
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 1156-Control-Hippocampusdim(obj@meta.data)## [1] 137679 118# get patient metadata
metadata_samples_all <- read.csv(metadata_all_path, sep='\t')
head(metadata_samples_all)## sample subject_id diagnosis brain_region sex age
## 1 1317-Bipolar-dACC 1317 Bipolar dACC Female 56.6
## 2 1320-Schizophrenia-DLPFC 1320 Schizophrenia DLPFC Male 53.2
## 3 1390-Control-dACC 1390 Control dACC Female 42.7
## 4 1713-Bipolar-dACC 1713 Bipolar dACC Male 20.7
## 5 1317-Bipolar-DLPFC 1317 Bipolar DLPFC Female 56.6
## 6 1390-Control-DLPFC 1390 Control DLPFC Female 42.7
## race ethnicity pulsar_id pmi_hours
## 1 White Not Hispanic or Latino 13957 26.50
## 2 Black or African-American Not Hispanic or Latino 13959 40.50
## 3 Black or African-American Not Hispanic or Latino 13963 8.17
## 4 White Not Hispanic or Latino 13996 26.50
## 5 White Not Hispanic or Latino 13956 26.50
## 6 Black or African-American Not Hispanic or Latino 13961 8.17
## tissue_pH RIN original_name swap batch SREQ
## 1 5.81 2.1 1317-Bipolar-dACC False 1 436/437
## 2 6.52 8.9 1320-Schizophrenia-DLPFC False 1 436/437
## 3 6.34 8.9 1390-Control-dACC False 1 436/437
## 4 6.45 7 1713-Bipolar-dACC False 1 436/437
## 5 5.81 N/A too low 1317-Bipolar-DLPFC False 2 439/440
## 6 6.34 7.7 1320-Schizophrenia-Hippocampus True 2 439/440
## who.nuclei_prep who.multiome date qc_rna qc_atac num_cells
## 1 Yiling Joan 10/13/2021 fail pass 7885
## 2 Yiling Joan 10/13/2021 pass pass 4763
## 3 Yiling Joan 10/13/2021 pass pass 2854
## 4 Yiling Joan 10/13/2021 borderline pass 7212
## 5 Yiling Minyi 10/22/2021 fail fail 5337
## 6 Yiling Minyi 10/22/2021 pass pass 7128
## mean_rna_reads mean_atac_reads median_high_quality_fragments tss_enrichment
## 1 25741.51 25952.11 5696.0 5.9193
## 2 40303.93 29276.88 8747.0 6.7518
## 3 65877.85 68351.57 11856.5 5.6492
## 4 28831.78 25978.22 4010.5 7.7729
## 5 21499.03 19824.73 4951.0 3.8609
## 6 12446.31 14240.00 4974.5 6.1892
## median_genes median_umi q30_rna q30_atac q30_all
## 1 112 160.0 0.9518203 0.9372318 0.9446584
## 2 1369 2452.0 0.9481870 0.9137288 0.9340603
## 3 2378 6267.5 0.9471261 0.9336242 0.9404008
## 4 244 274.0 0.9473116 0.9324500 0.9404322
## 5 463 766.0 0.9546507 0.9320030 0.9440367
## 6 1471 2821.0 0.9515652 0.9348879 0.9428508
## oak_path
## 1 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC
## 2 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC
## 3 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC
## 4 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC
## 5 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus
## outs_path
## 1 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC/SREQ-436-437-3_1317-Bipolar-dACC_outs/outs
## 2 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC/SREQ-436-437-4_1320-Schizophrenia-DLPFC_outs/outs
## 3 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC/SREQ-436-437-5_1390-Control-dACC_outs/outs
## 4 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC/SREQ-436-437-6_1713-Bipolar-dACC_outs/outs
## 5 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC/SREQ-439-440-1_1317-Bipolar-DLPFC_outs/outs
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus/SREQ-439-440-3_1320-Schizophrenia-Hippocampus_outs/outs
## metrics_csv
## 1 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC/SREQ-436-437-3_1317-Bipolar-dACC_outs/outs/summary.csv
## 2 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC/SREQ-436-437-4_1320-Schizophrenia-DLPFC_outs/outs/summary.csv
## 3 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC/SREQ-436-437-5_1390-Control-dACC_outs/outs/summary.csv
## 4 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC/SREQ-436-437-6_1713-Bipolar-dACC_outs/outs/summary.csv
## 5 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC/SREQ-439-440-1_1317-Bipolar-DLPFC_outs/outs/summary.csv
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus/SREQ-439-440-3_1320-Schizophrenia-Hippocampus_outs/outs/summary.csv
## raw_rna_counts
## 1 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC/SREQ-436-437-3_1317-Bipolar-dACC_outs/outs/raw_feature_bc_matrix.h5
## 2 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC/SREQ-436-437-4_1320-Schizophrenia-DLPFC_outs/outs/raw_feature_bc_matrix.h5
## 3 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC/SREQ-436-437-5_1390-Control-dACC_outs/outs/raw_feature_bc_matrix.h5
## 4 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC/SREQ-436-437-6_1713-Bipolar-dACC_outs/outs/raw_feature_bc_matrix.h5
## 5 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC/SREQ-439-440-1_1317-Bipolar-DLPFC_outs/outs/raw_feature_bc_matrix.h5
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus/SREQ-439-440-3_1320-Schizophrenia-Hippocampus_outs/outs/raw_feature_bc_matrix.h5
## filtered_rna_counts
## 1 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC/SREQ-436-437-3_1317-Bipolar-dACC_outs/outs/filtered_feature_bc_matrix.h5
## 2 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC/SREQ-436-437-4_1320-Schizophrenia-DLPFC_outs/outs/filtered_feature_bc_matrix.h5
## 3 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC/SREQ-436-437-5_1390-Control-dACC_outs/outs/filtered_feature_bc_matrix.h5
## 4 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC/SREQ-436-437-6_1713-Bipolar-dACC_outs/outs/filtered_feature_bc_matrix.h5
## 5 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC/SREQ-439-440-1_1317-Bipolar-DLPFC_outs/outs/filtered_feature_bc_matrix.h5
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus/SREQ-439-440-3_1320-Schizophrenia-Hippocampus_outs/outs/filtered_feature_bc_matrix.h5
## atac_fragments
## 1 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC/SREQ-436-437-3_1317-Bipolar-dACC_outs/outs/atac_fragments.tsv.gz
## 2 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC/SREQ-436-437-4_1320-Schizophrenia-DLPFC_outs/outs/atac_fragments.tsv.gz
## 3 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC/SREQ-436-437-5_1390-Control-dACC_outs/outs/atac_fragments.tsv.gz
## 4 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC/SREQ-436-437-6_1713-Bipolar-dACC_outs/outs/atac_fragments.tsv.gz
## 5 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC/SREQ-439-440-1_1317-Bipolar-DLPFC_outs/outs/atac_fragments.tsv.gz
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus/SREQ-439-440-3_1320-Schizophrenia-Hippocampus_outs/outs/atac_fragments.tsv.gz
## per_barcode_metrics
## 1 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC/SREQ-436-437-3_1317-Bipolar-dACC_outs/outs/per_barcode_metrics.csv
## 2 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC/SREQ-436-437-4_1320-Schizophrenia-DLPFC_outs/outs/per_barcode_metrics.csv
## 3 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC/SREQ-436-437-5_1390-Control-dACC_outs/outs/per_barcode_metrics.csv
## 4 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC/SREQ-436-437-6_1713-Bipolar-dACC_outs/outs/per_barcode_metrics.csv
## 5 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC/SREQ-439-440-1_1317-Bipolar-DLPFC_outs/outs/per_barcode_metrics.csv
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus/SREQ-439-440-3_1320-Schizophrenia-Hippocampus_outs/outs/per_barcode_metrics.csv
## gex_molecule_info
## 1 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC/SREQ-436-437-3_1317-Bipolar-dACC_outs/outs/gex_molecule_info.h5
## 2 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC/SREQ-436-437-4_1320-Schizophrenia-DLPFC_outs/outs/gex_molecule_info.h5
## 3 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC/SREQ-436-437-5_1390-Control-dACC_outs/outs/gex_molecule_info.h5
## 4 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC/SREQ-436-437-6_1713-Bipolar-dACC_outs/outs/gex_molecule_info.h5
## 5 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC/SREQ-439-440-1_1317-Bipolar-DLPFC_outs/outs/gex_molecule_info.h5
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus/SREQ-439-440-3_1320-Schizophrenia-Hippocampus_outs/outs/gex_molecule_info.h5dim(metadata_samples_all)## [1] 111 39# add patient metadata to cell metadata
cell_meta <- obj@meta.data
cell_meta <- left_join(cell_meta, metadata_samples_all %>%
dplyr::select(sample, condition = diagnosis,
region = brain_region, donor = subject_id,
batch, sex, age, race,
source = who.multiome), by = 'sample')
rownames(cell_meta) <- rownames(obj@meta.data)
# put our new metadata back
obj@meta.data <- cell_meta
head(obj@meta.data)## orig.ident nCount_RNA
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 1156-Control-Hippocampus 145402
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 1156-Control-Hippocampus 139613
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 1156-Control-Hippocampus 134099
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 1156-Control-Hippocampus 127166
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 1156-Control-Hippocampus 121561
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 1156-Control-Hippocampus 115519
## nFeature_RNA barcode
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 10646 CAAACCGTCTGTTCAT-1
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 10253 AGTACGCGTTTGGCGG-1
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 10251 GGATTTATCCTCGATC-1
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 10544 CGTAACCCAAGCTAAA-1
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 9714 ATGTAACGTCTTGCTG-1
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 10540 CATCCTGGTATTGGAT-1
## gex_barcode
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 CAAACCGTCTGTTCAT-1
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 AGTACGCGTTTGGCGG-1
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 GGATTTATCCTCGATC-1
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 CGTAACCCAAGCTAAA-1
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 ATGTAACGTCTTGCTG-1
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 CATCCTGGTATTGGAT-1
## atac_barcode is_cell
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 GGCTAATAGTTAGTAG-1 1
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 CCTGGTCCACATGCTT-1 1
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 CAGTGTGAGAACCTGG-1 1
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 AGCTTGTGTAATCGCT-1 1
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 GAAGGTGCATGGATAT-1 1
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 AACCGCGCATTACTGC-1 1
## excluded_reason gex_raw_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0 343330
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0 318177
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0 327874
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0 297819
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0 266038
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0 295263
## gex_mapped_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 329771
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 305565
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 315601
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 285747
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 255061
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 283993
## gex_conf_intergenic_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 27732
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 25282
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 23446
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 25110
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 22349
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 24129
## gex_conf_exonic_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 37587
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 36708
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 34621
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 35467
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 29635
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 36983
## gex_conf_intronic_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 250122
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 230991
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 245826
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 213166
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 191574
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 211530
## gex_conf_exonic_unique_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 33186
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 32906
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 29898
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 31995
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 26800
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 31843
## gex_conf_exonic_antisense_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 4119
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 3534
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 4478
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 3259
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 2639
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 4880
## gex_conf_exonic_dup_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 13535
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 13200
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 12266
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 12805
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 10105
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 13059
## gex_exonic_umis
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 19178
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 19209
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 17207
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 18683
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 16272
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 18338
## gex_conf_intronic_unique_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 221898
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 207306
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 211042
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 190491
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 174349
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 174580
## gex_conf_intronic_antisense_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 23916
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 19321
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 30837
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 19009
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 13847
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 33714
## gex_conf_intronic_dup_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 92875
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 83865
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 91480
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 79442
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 66730
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 75142
## gex_intronic_umis
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 126253
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 120439
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 116918
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 108499
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 105323
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 97214
## gex_conf_txomic_unique_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 31216
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 30813
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 28008
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 30081
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 25370
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 30070
## gex_umis_count gex_genes_count
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0 0
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0 0
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0 0
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0 0
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0 0
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0 0
## atac_raw_reads atac_unmapped_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 43360 254
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 11995 70
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 51227 276
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 69610 388
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 20392 98
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 76448 346
## atac_lowmapq atac_dup_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 2967 13501
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 1226 3503
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 3209 16879
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 4598 23065
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 1848 6951
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 5046 25534
## atac_chimeric_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 48
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 21
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 43
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 83
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 27
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 74
## atac_mitochondrial_reads
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 171
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 2
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 49
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 318
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 79
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 320
## atac_fragments atac_TSS_fragments
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 26410 4703
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 7150 957
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 30758 5640
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 41119 7474
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 11352 1772
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 45094 8692
## atac_peak_region_fragments
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 4471
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 817
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 5226
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 6110
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 1499
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 8677
## atac_peak_region_cutsites
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 7931
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 1452
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 9198
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 10691
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 2649
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 15378
## nCount_ATAC nFeature_ATAC
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 10784 9788
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 2188 2138
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 13201 11890
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 14935 12864
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 3920 3753
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 20516 17489
## nucleosome_signal
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 1.6092156
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0.9012915
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 1.5591801
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 1.3148219
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 1.0151515
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 1.3918440
## nucleosome_percentile
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0.98
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0.70
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0.98
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0.93
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0.80
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0.95
## TSS.enrichment TSS.percentile
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 3.102337 0.47
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 2.268102 0.35
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 2.617383 0.39
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 2.983224 0.44
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 2.405214 0.37
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 2.971033 0.44
## pct_frags_in_peaks percent.mt
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 16.92919 0.4711077
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 11.42657 0.0250693
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 16.99070 0.1603293
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 14.85931 0.1981662
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 13.20472 0.1785112
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 19.24203 0.6665570
## nCount_SCT nFeature_SCT
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 5105 2608
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 5441 2518
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 5090 2578
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 6430 2990
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 5327 2319
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 5339 2883
## nCount_refAssay nFeature_refAssay
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 145402 10646
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 139613 10253
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 134099 10251
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 127166 10544
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 121561 9714
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 115519 10540
## predicted.class.score
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 1
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 1
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 1
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 1
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 1
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 1
## predicted.class
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 Glutamatergic
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 Glutamatergic
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 Glutamatergic
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 GABAergic
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 Glutamatergic
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 Glutamatergic
## predicted.cluster.score
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0.2749085
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0.2927073
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0.3032498
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0.5728458
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0.2601393
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0.2714480
## predicted.cluster
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 Exc L2 LAMP5 KCNG3
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 Exc L2 LAMP5 KCNG3
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 Exc L2 LAMP5 KCNG3
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 Inh L1-3 SST FAM20A
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 Exc L2 LAMP5 KCNG3
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 Exc L2 LAMP5 KCNG3
## predicted.subclass.score
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0.5874844
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0.5648823
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0.6244408
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0.8180437
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0.5697701
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0.5908260
## predicted.subclass
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 L2/3 IT
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 L2/3 IT
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 L2/3 IT
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 Sst
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 L2/3 IT
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 L2/3 IT
## predicted.cross_species_cluster.score
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0.5874844
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0.5648823
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0.6244408
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0.7974378
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0.5697701
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0.5908260
## predicted.cross_species_cluster
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 L2/3 IT
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 L2/3 IT
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 L2/3 IT
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 Sst_3
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 L2/3 IT
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 L2/3 IT
## mapping.score SCT_snn_res.0.8
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0.4803418 14
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0.6165295 14
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0.4102896 14
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0.9942214 10
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0.6244192 14
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0.4495509 14
## seurat_clusters atac_doublets
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 14 singlet
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 14 singlet
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 14 singlet
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 10 singlet
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 14 singlet
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 14 singlet
## pANN_0.25_0.01_35
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 0.2758621
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 0.2413793
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 0.2068966
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 0.2413793
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 0.2413793
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 0.2413793
## DF.classifications_0.25_0.01_35
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 Singlet
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 Singlet
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 Singlet
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 Singlet
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 Singlet
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 Singlet
## rna_doublets all_doublets
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 singlet singlet
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 singlet singlet
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 singlet singlet
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 singlet singlet
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 singlet singlet
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 singlet singlet
## region.x pANN_0.25_0.01_293
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 Hippocampus NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 Hippocampus NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 Hippocampus NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 Hippocampus NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 Hippocampus NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 Hippocampus NA
## DF.classifications_0.25_0.01_293
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_215
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_215
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_295
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_295
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_410
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_410
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_122
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_122
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_289
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_289
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_141
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_141
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_134
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_134
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_30
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_30
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_64
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_64
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_199
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_199
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_283
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_283
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_203
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_203
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_272
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_272
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_652
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_652
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_268
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_268
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_182
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_182
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_36
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_36
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_65
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_65
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_71
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_71
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_117
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_117
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_408
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_408
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_285
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_285
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_113
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_113
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_379
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_379
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_201
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_201
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## pANN_0.25_0.01_138
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 NA
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 NA
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 NA
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 NA
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 NA
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 NA
## DF.classifications_0.25_0.01_138
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 <NA>
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 <NA>
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 <NA>
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 <NA>
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 <NA>
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 <NA>
## sample condition
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 1156-Control-Hippocampus Control
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 1156-Control-Hippocampus Control
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 1156-Control-Hippocampus Control
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 1156-Control-Hippocampus Control
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 1156-Control-Hippocampus Control
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 1156-Control-Hippocampus Control
## region.y donor batch sex age
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 Hippocampus 1156 23 Female 53.9
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 Hippocampus 1156 23 Female 53.9
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 Hippocampus 1156 23 Female 53.9
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 Hippocampus 1156 23 Female 53.9
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 Hippocampus 1156 23 Female 53.9
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 Hippocampus 1156 23 Female 53.9
## race source
## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1 Black or African-American Joan
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1 Black or African-American Joan
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1 Black or African-American Joan
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1 Black or African-American Joan
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1 Black or African-American Joan
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1 Black or African-American JoanPreprocessing without batch correction
Idents(obj) <- 'sample'RNA
# normalize data using the standard scaling/log-transform
DefaultAssay(obj) <- "RNA"
obj <- NormalizeData(obj, normalization.method = "LogNormalize",
scale.factor = 10000)
# find variable genes and scale data
obj <- FindVariableFeatures(obj, selection.method = "vst", nfeatures = 2000)
# Identify the 10 most highly variable genes
top10 <- head(VariableFeatures(obj), 10)
# SCT
obj <- SCTransform(obj,
new.assay.name = "SCT",
verbose = T)## Calculating cell attributes from input UMI matrix: log_umi## Variance stabilizing transformation of count matrix of size 33531 by 137679## Model formula is y ~ log_umi## Get Negative Binomial regression parameters per gene## Using 2000 genes, 5000 cells## | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100%## Found 84 outliers - those will be ignored in fitting/regularization step## Second step: Get residuals using fitted parameters for 33531 genes## | | | 0% | |= | 1% | |== | 3% | |=== | 4% | |==== | 6% | |===== | 7% | |====== | 9% | |======= | 10% | |======== | 12% | |========= | 13% | |========== | 15% | |=========== | 16% | |============ | 18% | |============= | 19% | |============== | 21% | |=============== | 22% | |================ | 24% | |================== | 25% | |=================== | 26% | |==================== | 28% | |===================== | 29% | |====================== | 31% | |======================= | 32% | |======================== | 34% | |========================= | 35% | |========================== | 37% | |=========================== | 38% | |============================ | 40% | |============================= | 41% | |============================== | 43% | |=============================== | 44% | |================================ | 46% | |================================= | 47% | |================================== | 49% | |=================================== | 50% | |==================================== | 51% | |===================================== | 53% | |====================================== | 54% | |======================================= | 56% | |======================================== | 57% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 62% | |============================================ | 63% | |============================================= | 65% | |============================================== | 66% | |=============================================== | 68% | |================================================ | 69% | |================================================= | 71% | |================================================== | 72% | |=================================================== | 74% | |==================================================== | 75% | |====================================================== | 76% | |======================================================= | 78% | |======================================================== | 79% | |========================================================= | 81% | |========================================================== | 82% | |=========================================================== | 84% | |============================================================ | 85% | |============================================================= | 87% | |============================================================== | 88% | |=============================================================== | 90% | |================================================================ | 91% | |================================================================= | 93% | |================================================================== | 94% | |=================================================================== | 96% | |==================================================================== | 97% | |===================================================================== | 99% | |======================================================================| 100%## Computing corrected count matrix for 33531 genes## | | | 0% | |= | 1% | |== | 3% | |=== | 4% | |==== | 6% | |===== | 7% | |====== | 9% | |======= | 10% | |======== | 12% | |========= | 13% | |========== | 15% | |=========== | 16% | |============ | 18% | |============= | 19% | |============== | 21% | |=============== | 22% | |================ | 24% | |================== | 25% | |=================== | 26% | |==================== | 28% | |===================== | 29% | |====================== | 31% | |======================= | 32% | |======================== | 34% | |========================= | 35% | |========================== | 37% | |=========================== | 38% | |============================ | 40% | |============================= | 41% | |============================== | 43% | |=============================== | 44% | |================================ | 46% | |================================= | 47% | |================================== | 49% | |=================================== | 50% | |==================================== | 51% | |===================================== | 53% | |====================================== | 54% | |======================================= | 56% | |======================================== | 57% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 62% | |============================================ | 63% | |============================================= | 65% | |============================================== | 66% | |=============================================== | 68% | |================================================ | 69% | |================================================= | 71% | |================================================== | 72% | |=================================================== | 74% | |==================================================== | 75% | |====================================================== | 76% | |======================================================= | 78% | |======================================================== | 79% | |========================================================= | 81% | |========================================================== | 82% | |=========================================================== | 84% | |============================================================ | 85% | |============================================================= | 87% | |============================================================== | 88% | |=============================================================== | 90% | |================================================================ | 91% | |================================================================= | 93% | |================================================================== | 94% | |=================================================================== | 96% | |==================================================================== | 97% | |===================================================================== | 99% | |======================================================================| 100%## Calculating gene attributes## Wall clock passed: Time difference of 11.22795 mins## Determine variable features## Place corrected count matrix in counts slot## Centering data matrix## Set default assay to SCTobj <- RunPCA(obj,
assay = "SCT",
reduction.name = 'pca',
reduction.key = "PC"
)## PC_ 1
## Positive: KCNIP4, CSMD1, RBFOX1, SYT1, LHFPL3, DLGAP1, MEG3, OPCML, STXBP5L, FAM155A
## ST6GALNAC5, CNTNAP2, SNTG1, SNHG14, RYR2, CADM2, CLSTN2, CSMD3, PPM1E, CNTN5
## ROBO2, DAB1, LRRTM4, GRIA1, GRIK2, DLGAP2, NXPH1, GRM7, FGF14, LRRC7
## Negative: HTR2C, OTX2-AS1, TTR, LRMDA, CFAP299, DOCK8, PRLR, TRPM3, DNAH11, ARHGAP24
## TRMT9B, APBB1IP, RMST, AL163541.1, RBM47, SULF1, ADAM28, SLC13A4, IGFBP7, AC016152.1
## LNCAROD, CLIC6, ADGB, ARMC3, GRM8, AC019197.1, AC092957.1, ROR2, SPAG17, COBLL1
## PC_ 2
## Positive: LRMDA, APBB1IP, ARHGAP24, AL163541.1, ADAM28, LNCAROD, FYB1, AC008691.1, P2RY12, DOCK8
## ST6GAL1, TBXAS1, INPP5D, DLEU1, ARHGAP15, LINC02712, RUNX1, CPED1, SYNDIG1, SLCO2B1
## IPCEF1, SPP1, DOCK2, RASGEF1C, SAMSN1, PLXDC2, LINC01374, MSR1, SYK, MEF2C
## Negative: HTR2C, OTX2-AS1, CFAP299, TRPM3, TTR, PRLR, DNAH11, TRMT9B, DPP10, RMST
## GRM8, ADGB, ARMC3, SULF1, CFAP54, AC016152.1, CLIC6, SLC13A4, SPAG17, CFAP47
## IGFBP7, AC020718.1, AC019197.1, LINC01088, DCDC1, AC092957.1, DTHD1, PCAT1, GPC5, AC019330.1
## PC_ 3
## Positive: CTNNA3, ST18, AC012494.1, RNF220, MOBP, AC008571.2, GPC5, IL1RAPL1, MBP, PLP1
## AL033523.1, LINC01608, PCDH9, SLC5A11, SLC7A14-AS1, TMEM144, TMTC2, QKI, TF, AC012405.1
## OBI1-AS1, DPP10, MAN2A1, AC090015.1, PIP4K2A, PPP2R2B, C10orf90, LINC00609, PDE1C, KCNH8
## Negative: KCNIP4, CSMD1, RBFOX1, SYT1, HTR2C, ROBO2, DLGAP1, LRMDA, MEG3, OPCML
## STXBP5L, FAM155A, FRMD4A, SNHG14, ST6GALNAC5, LHFPL3, SNTG1, CSMD3, DOCK8, CCSER1
## CNTN5, TRPM3, CNTNAP2, CLSTN2, GRIA1, FGF14, APBB1IP, PPM1E, NELL2, GALNTL6
## PC_ 4
## Positive: DPP10, GPC5, AC012405.1, OBI1-AS1, SLC1A2, AC002429.2, ADGRV1, HPSE2, CTNNA2, LINC00299
## MIR4300HG, FAM189A2, PITPNC1, BMPR1B, TNC, ALDH1A1, MGAT4C, RFX4, NRXN1, GPM6A
## SOX5, AL137139.2, AC114971.1, SPARCL1, AC073941.1, SLC14A1, NRG3, GFAP, GLIS3, LINC00499
## Negative: HTR2C, OTX2-AS1, TTR, PRLR, TRMT9B, GRM8, AC016152.1, SLC13A4, TRPM3, CTNNA3
## AC019197.1, CLIC6, SULF1, COBLL1, IL1RAPL1, AC004052.1, ST18, AC092957.1, RBM47, ABCA4
## ROR2, AC012494.1, RNF220, GULP1, PIP5K1B, IGFBP7, PLD5, MOBP, AC008571.2, CUX2
## PC_ 5
## Positive: HTR2C, GPC5, OTX2-AS1, TTR, TRPM3, PRLR, LHFPL3, OBI1-AS1, SLC1A2, GRM8
## TRMT9B, SLC13A4, AC016152.1, IGFBP7, AC019197.1, AC002429.2, SULF1, COBLL1, NXPH1, CLIC6
## ABCA4, RBM47, FYB2, PDZRN3, PIP5K1B, ADGRV1, GULP1, LINC00299, CUX2, PDK4
## Negative: CFAP299, AC020718.1, DTHD1, AC019330.1, TTC6, ADGB, CFAP47, AGBL1, LINC02055, TTC29
## AC004949.1, DNAH9, SPAG17, CFAP54, DCDC1, DNAH11, ARMC3, DNAH12, DNAH3, LMNTD1
## CFAP43, AL357093.2, AC013470.2, CASC15, SPATA17, ARMC4, ZBBX, MAP3K19, LRRC9, TCTEX1D1ElbowPlot(obj, reduction = "pca")
ATAC
DefaultAssay(obj) <- "ATAC"
obj <- FindTopFeatures(obj)
obj <- RunTFIDF(obj)## Performing TF-IDF normalizationobj <- RunSVD(obj,
reduction.key = "LSI",
reduction.name = "lsi")## Running SVD## Scaling cell embeddingsDefaultAssay(obj) <- "ATAC"
DepthCor(obj,
reduction = "lsi")
obj## An object of class Seurat
## 388366 features across 137679 samples within 3 assays
## Active assay: ATAC (318234 features, 302522 variable features)
## 2 layers present: counts, data
## 2 other assays present: RNA, SCT
## 2 dimensional reductions calculated: pca, lsiDimensionality reduction and clustering
# build a joint neighbor graph using both assays
obj <- FindMultiModalNeighbors(
object = obj,
reduction.list = list("pca", "lsi"),
knn.graph.name = "wknn",
snn.graph.name = "wsnn",
weighted.nn.name = "weighted.nn",
dims.list = list(1:50, 2:50),
verbose = TRUE
)## Calculating cell-specific modality weights## Finding 20 nearest neighbors for each modality.## Calculating kernel bandwidths## Finding multimodal neighbors## Constructing multimodal KNN graph## Constructing multimodal SNN graph# build a joint UMAP visualization
obj <- RunUMAP(
object = obj,
nn.name = "weighted.nn",
reduction.name = "wnn.umap",
reduction.key = "wnnUMAP_",
verbose = TRUE
)## 07:29:47 UMAP embedding parameters a = 0.9922 b = 1.112## 07:29:49 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 20
## 07:29:50 3 smooth knn distance failures
## 07:29:53 Initializing from normalized Laplacian + noise (using irlba)
## 07:30:30 Commencing optimization for 200 epochs, with 4535322 positive edges
## 07:31:42 Optimization finished# cluster over neighbor graph
obj <- FindClusters(
object = obj,
algorithm = 4,
resolution = 0.6,
graph.name = 'wsnn',
verbose = TRUE,
method = "igraph"
)## 103 singletons identified. 36 final clusters.# visualize data
DimPlot(obj,
pt.size = 1,
label.size = 0,
reduction = "wnn.umap",
group.by = 'batch',
raster = TRUE)## Rasterizing points since number of points exceeds 100,000.
## To disable this behavior set `raster=FALSE`
# barplot of cluster breakdown by sample
obj@meta.data %>%
ggplot(aes(x = seurat_clusters)) +
geom_bar(aes(fill = sample), position = "fill") +
ggtitle("Breakdown of clusters by sample")
# barplot of cluster breakdown by batch
obj@meta.data %>%
mutate(batch = factor(batch)) %>%
ggplot(aes(x = seurat_clusters)) +
geom_bar(aes(fill = batch), position = "fill") +
ggtitle("Breakdown of clusters by batch")
Reference-based cell type annotation using Azimuth
DefaultAssay(obj) <- "SCT"
obj_mock <- RunAzimuth(obj,
reference = "humancortexref",
assay="SCT",
umap.name = "ref.umap") ## detected inputs from HUMAN with id type Gene.name## reference rownames detected HUMAN with id type Gene.name## Using reference SCTModel to calculate pearson residuals## Determine variable features## Setting min_variance to: -Inf## Calculating residuals of type pearson for 2216 genes## | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100%## Set default assay to refAssay## Normalizing query using reference SCT model## Projecting cell embeddings## Finding query neighbors## Finding neighborhoods## Finding anchors## Found 8393 anchors## Finding integration vectors## Finding integration vector weights## Predicting cell labels
## Predicting cell labels
## Predicting cell labels
## Predicting cell labels##
## Integrating dataset 2 with reference dataset## Finding integration vectors## Integrating data## Computing nearest neighbors## Running UMAP projection## 07:43:25 Read 137679 rows## 07:43:25 Processing block 1 of 1## 07:43:25 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 20
## 07:43:26 Initializing by weighted average of neighbor coordinates using 1 thread
## 07:43:26 Commencing optimization for 67 epochs, with 2753580 positive edges
## 07:43:40 Finished
## Projecting reference PCA onto query
## Finding integration vector weights
## Projecting back the query cells into original PCA space
## Finding integration vector weights
## Computing scores:
## Finding neighbors of original query cells
## Finding neighbors of transformed query cells
## Computing query SNN
## Determining bandwidth and computing transition probabilities
## Total elapsed time: 1.74682185649872predicted.subclass.before.harmony <- obj_mock$predicted.subclass
head(predicted.subclass.before.harmony)## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1
## "L2/3 IT"
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1
## "L5 ET"
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1
## "L2/3 IT"
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1
## "Sst"
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1
## "L5 ET"
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1
## "L2/3 IT"length(predicted.subclass.before.harmony)## [1] 137679rm(obj_mock)Run Harmony batch correction using batch column
obj@meta.data$batch <- as.factor(obj@meta.data$batch)
DefaultAssay(obj) <- "SCT"
obj_harmony <- RunHarmony(
object = obj,
group.by.vars = 'batch',
reduction = 'pca',
assay.use = 'SCT',
reduction.save = "harmony_sct_batch",
project.dim = FALSE
)## Transposing data matrix## Initializing state using k-means centroids initialization## Harmony 1/10## Harmony 2/10## Harmony 3/10## Harmony 4/10## Harmony 5/10## Harmony 6/10## Harmony 7/10## Harmony 8/10## Harmony converged after 8 iterationsDefaultAssay(obj_harmony) <- "ATAC"
obj_harmony <- RunHarmony(
object = obj_harmony,
group.by.vars = 'batch',
reduction = 'lsi',
assay.use = 'ATAC',
reduction.save = "harmony_atac_batch",
project.dim = FALSE
)## Transposing data matrix## Initializing state using k-means centroids initialization## Harmony 1/10## Harmony 2/10## Harmony 3/10## Harmony 4/10## Harmony 5/10## Harmony 6/10## Harmony 7/10## Harmony 8/10## Harmony 9/10## Harmony 10/10# build a joint neighbor graph using both assays
obj_harmony <- FindMultiModalNeighbors(
object = obj_harmony,
reduction.list = list("harmony_sct_batch", "harmony_atac_batch"),
knn.graph.name = "wknn_batch",
snn.graph.name = "wsnn_batch",
weighted.nn.name = "weighted.nn_batch",
dims.list = list(1:50, 2:50),
verbose = TRUE
)## Calculating cell-specific modality weights## Finding 20 nearest neighbors for each modality.## Calculating kernel bandwidths## Finding multimodal neighbors## Constructing multimodal KNN graph## Constructing multimodal SNN graph# build a joint UMAP visualization
obj_harmony <- RunUMAP(
object = obj_harmony,
nn.name = "weighted.nn_batch",
reduction.name = "harm.wnn.umap_batch",
reduction.key = "harm.batch.wnnUMAP_",
verbose = TRUE
)## 08:04:26 UMAP embedding parameters a = 0.9922 b = 1.112## 08:04:29 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 20
## 08:04:29 4 smooth knn distance failures
## 08:04:32 Initializing from normalized Laplacian + noise (using irlba)
## 08:04:49 Commencing optimization for 200 epochs, with 4626676 positive edges
## 08:05:56 Optimization finishedAzimuth
# first with the human reference (same as other brain regions)
DefaultAssay(obj_harmony) <- "SCT"
obj_harmony <- RunAzimuth(obj_harmony,
reference = "humancortexref",
assay="SCT",
umap.name = "ref.umap") ## detected inputs from HUMAN with id type Gene.name## reference rownames detected HUMAN with id type Gene.name## Using reference SCTModel to calculate pearson residuals## Determine variable features## Setting min_variance to: -Inf## Calculating residuals of type pearson for 2216 genes## | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100%## Set default assay to refAssay## Normalizing query using reference SCT model## Projecting cell embeddings## Finding query neighbors## Finding neighborhoods## Finding anchors## Found 8393 anchors## Finding integration vectors## Finding integration vector weights## Predicting cell labels
## Predicting cell labels
## Predicting cell labels
## Predicting cell labels##
## Integrating dataset 2 with reference dataset## Finding integration vectors## Integrating data## Computing nearest neighbors## Running UMAP projection## 08:10:45 Read 137679 rows## 08:10:45 Processing block 1 of 1## 08:10:45 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 20
## 08:10:46 Initializing by weighted average of neighbor coordinates using 1 thread
## 08:10:46 Commencing optimization for 67 epochs, with 2753580 positive edges
## 08:11:00 Finished
## Projecting reference PCA onto query
## Finding integration vector weights
## Projecting back the query cells into original PCA space
## Finding integration vector weights
## Computing scores:
## Finding neighbors of original query cells
## Finding neighbors of transformed query cells
## Computing query SNN
## Determining bandwidth and computing transition probabilities
## Total elapsed time: 1.67758725881577# rename columns to not overwrite in next run of azimuth with diff reference
colnames(obj_harmony@meta.data)[colnames(obj_harmony@meta.data) == 'predicted.class'] <- 'predicted.class__humancortexref'
colnames(obj_harmony@meta.data)[colnames(obj_harmony@meta.data) == 'predicted.class.score'] <- 'predicted.class.score__humancortexref'
colnames(obj_harmony@meta.data)[colnames(obj_harmony@meta.data) == 'predicted.cluster'] <- 'predicted.cluster__humancortexref'
colnames(obj_harmony@meta.data)[colnames(obj_harmony@meta.data) == 'predicted.cluster.score'] <- 'predicted.cluster.score__humancortexref'
colnames(obj_harmony@meta.data)[colnames(obj_harmony@meta.data) == 'predicted.subclass'] <- 'predicted.subclass__humancortexref'
colnames(obj_harmony@meta.data)[colnames(obj_harmony@meta.data) == 'predicted.subclass.score'] <- 'predicted.subclass.score__humancortexref'
colnames(obj_harmony@meta.data)[colnames(obj_harmony@meta.data) == 'predicted.cross_species_cluster'] <- 'predicted.cross_species_cluster__humancortexref'
colnames(obj_harmony@meta.data)[colnames(obj_harmony@meta.data) == 'predicted.cross_species_cluster.score'] <- 'predicted.cross_species_cluster.score__humancortexref'# with human hippocampus ref
obj_harmony <- RunAzimuth(obj_harmony,
reference = "/users/guozy/psychencode/outs/20231009_multiome_analysis/03-integration/hippocampus_reference/Franjic2022/",
assay="SCT",
umap.name = "ref.umap")## detected inputs from HUMAN with id type Gene.name## reference rownames detected HUMAN with id type Gene.name## Using reference SCTModel to calculate pearson residuals## Determine variable features## Setting min_variance based on median UMI: 0.16## Calculating residuals of type pearson for 2943 genes## | | | 0% | |====== | 8% | |============ | 17% | |================== | 25% | |======================= | 33% | |============================= | 42% | |=================================== | 50% | |========================================= | 58% | |=============================================== | 67% | |==================================================== | 75% | |========================================================== | 83% | |================================================================ | 92% | |======================================================================| 100%## Set default assay to refAssay## Normalizing query using reference SCT model## Projecting cell embeddings## Finding query neighbors## Finding neighborhoods## Finding anchors## Found 80189 anchors## Finding integration vectors## Finding integration vector weights## Predicting cell labels
## Predicting cell labels##
## Integrating dataset 2 with reference dataset## Finding integration vectors## Integrating data## Computing nearest neighbors## Running UMAP projection## 08:20:37 Read 137679 rows## 08:20:37 Processing block 1 of 1## 08:20:37 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 20
## 08:20:38 Initializing by weighted average of neighbor coordinates using 1 thread
## 08:20:38 Commencing optimization for 67 epochs, with 2753580 positive edges
## 08:20:53 Finished
## Projecting reference PCA onto query
## Finding integration vector weights
## Projecting back the query cells into original PCA space
## Finding integration vector weights
## Computing scores:
## Finding neighbors of original query cells
## Finding neighbors of transformed query cells
## Computing query SNN
## Determining bandwidth and computing transition probabilities
## Total elapsed time: 2.69056731859843DimPlot(obj_harmony, shuffle=TRUE, label = FALSE, repel = TRUE, pt.siz=1,
label.size=0, reduction = "harm.wnn.umap_batch",
group.by = 'predicted.subclass__humancortexref', raster=FALSE) +
theme(legend.text = element_text(size=30), plot.title = element_text(size=40),
axis.title = element_text(size=30))
DimPlot(obj_harmony, shuffle=TRUE, label = FALSE, repel = TRUE, pt.siz=1,
label.size=0, reduction = "harm.wnn.umap_batch",
group.by = 'predicted.cluster_broad', raster=FALSE) +
theme(legend.text = element_text(size=30), plot.title = element_text(size=40),
axis.title = element_text(size=30))
# Check whether labels (from the human ctx ref) are independent of Harmony
# If TRUE, Azimuth labels do not depend on Harmony-corrected PCA embedding (of SCT data)
setequal(predicted.subclass.before.harmony,
obj_harmony$predicted.subclass__humancortexref)## [1] TRUELeiden clustering
obj_harmony <- FindClusters(
object = obj_harmony,
algorithm = 4,
resolution = 0.6,
graph.name = 'wsnn_batch',
verbose = TRUE,
method = "igraph"
)## 160 singletons identified. 31 final clusters.table(obj_harmony$seurat_clusters)##
## 1 2 3 4 5 6 7 8 9 10 11 12 13
## 22299 14575 14126 11886 11143 11081 9680 8916 6765 4367 4281 2242 2161
## 14 15 16 17 18 19 20 21 22 23 24 25 26
## 2148 1574 1370 1235 1302 1110 1009 1006 1002 821 731 266 265
## 27 28 29 30 31
## 117 72 65 62 2head(obj_harmony$seurat_clusters)## 1156-Control-Hippocampus_CAAACCGTCTGTTCAT-1
## 7
## 1156-Control-Hippocampus_AGTACGCGTTTGGCGG-1
## 7
## 1156-Control-Hippocampus_GGATTTATCCTCGATC-1
## 7
## 1156-Control-Hippocampus_CGTAACCCAAGCTAAA-1
## 22
## 1156-Control-Hippocampus_ATGTAACGTCTTGCTG-1
## 7
## 1156-Control-Hippocampus_CATCCTGGTATTGGAT-1
## 7
## 31 Levels: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 ... 31# sanity check
all(Idents(obj_harmony) == obj_harmony@meta.data$seurat_cluster)## [1] TRUEall(obj_harmony@meta.data$seurat_clusters == obj_harmony@meta.data$seurat_cluster)## [1] TRUEDimPlot(obj_harmony, shuffle=TRUE, label = TRUE, repel = TRUE, pt.siz=1,
label.size=0, reduction = "harm.wnn.umap_batch",
group.by = 'seurat_clusters', raster=FALSE) +
theme(legend.text = element_text(size=30), plot.title = element_text(size=40),
axis.title = element_text(size=30))
Visualize batch-corrected data
# barplot of cluster breakdown by sample
obj_harmony@meta.data %>%
ggplot(aes(x = seurat_clusters)) +
geom_bar(aes(fill = sample), position = "fill") +
ggtitle("Breakdown of clusters by sample")
# barplot of cluster breakdown by batch
obj_harmony@meta.data %>%
mutate(batch = factor(batch)) %>%
ggplot(aes(x = seurat_clusters)) +
geom_bar(aes(fill = batch), position = "fill") +
ggtitle("Breakdown of clusters by batch")
By condition
# batch
DimPlot(obj_harmony, shuffle=TRUE, label = TRUE, repel = TRUE, pt.siz=1,
label.size=0, reduction = "harm.wnn.umap_batch",
group.by = 'condition', raster=FALSE) +
theme(legend.text = element_text(size=30), plot.title = element_text(size=40),
axis.title = element_text(size=30))
By sample
# batch
DimPlot(obj_harmony, shuffle=TRUE, label = TRUE, repel = TRUE, pt.siz=1,
label.size=0, reduction = "harm.wnn.umap_batch",
group.by = 'sample', raster=FALSE) +
theme(plot.title = element_text(size=40), axis.title = element_text(size=30)) +
NoLegend()
By ‘batch’
DimPlot(obj_harmony, shuffle=TRUE, label = TRUE, repel = TRUE, pt.siz=1,
label.size=0, reduction = "harm.wnn.umap_batch",
group.by = 'batch', raster=FALSE) +
theme(plot.title = element_text(size=40), axis.title = element_text(size=30))