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(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 <- 'dACC'
data_dir = '/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/dACC.merged.multiome.rds"obj <- readRDS(integrated_object_path)
obj## An object of class Seurat
## 315545 features across 124063 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 nFeature_RNA
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 1156-Control-dACC 89750 9397
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 1156-Control-dACC 88671 9644
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 1156-Control-dACC 88556 9266
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 1156-Control-dACC 87620 9258
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 1156-Control-dACC 84874 9106
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 1156-Control-dACC 81592 8503
## barcode gex_barcode
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 GAGTGATCAGAATGAC-1 GAGTGATCAGAATGAC-1
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 GAGCTGCTCATTCATC-1 GAGCTGCTCATTCATC-1
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 GAAAGGCTCCTTAAGA-1 GAAAGGCTCCTTAAGA-1
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 ATTTAGGTCATGCTAA-1 ATTTAGGTCATGCTAA-1
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 CTCCTCACAGCAATAA-1 CTCCTCACAGCAATAA-1
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 ACGATTCAGCTTCTCA-1 ACGATTCAGCTTCTCA-1
## atac_barcode is_cell excluded_reason
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 ACATTGCGTCTTAGCG-1 1 0
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 TCAAGCGAGACAAGCT-1 1 0
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 GATCAGTAGCCAAACG-1 1 0
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 ATGTCCCAGCTCGACT-1 1 0
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 GTGAACAGTACGTTTA-1 1 0
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 ATGCAAATCTTTAGGT-1 1 0
## gex_raw_reads gex_mapped_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 531010 504121
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 440213 411738
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 478967 451114
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 478048 453252
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 455765 432478
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 436191 415143
## gex_conf_intergenic_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 40409
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 35765
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 37825
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 39712
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 37188
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 31299
## gex_conf_exonic_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 62980
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 68829
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 68563
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 65365
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 71163
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 60555
## gex_conf_intronic_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 363846
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 263836
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 300171
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 315532
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 284694
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 290372
## gex_conf_exonic_unique_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 58101
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 64660
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 63483
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 60576
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 66418
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 56122
## gex_conf_exonic_antisense_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 4622
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 3790
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 4681
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 4447
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 4425
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 4103
## gex_conf_exonic_dup_reads gex_exonic_umis
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 45440 11877
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 48522 15293
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 48439 14106
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 46516 13211
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 51363 14203
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 43648 11812
## gex_conf_intronic_unique_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 337023
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 244322
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 278943
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 292515
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 263862
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 270905
## gex_conf_intronic_antisense_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 20066
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 14859
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 16116
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 17517
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 14384
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 13103
## gex_conf_intronic_dup_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 254687
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 166967
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 199519
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 213638
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 189515
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 197572
## gex_intronic_umis
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 77879
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 73393
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 74472
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 74426
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 70687
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 69814
## gex_conf_txomic_unique_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 54465
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 61779
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 60101
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 57737
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 63376
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 53181
## gex_umis_count gex_genes_count
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0 0
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0 0
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0 0
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0 0
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0 0
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 0 0
## atac_raw_reads atac_unmapped_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 43070 364
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 59998 467
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 30538 213
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 14037 116
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 1717 29
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 55627 450
## atac_lowmapq atac_dup_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 2584 15627
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 3573 19594
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 1982 10270
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 962 4829
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 162 532
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 4374 19082
## atac_chimeric_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 50
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 61
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 34
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 20
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 3
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 85
## atac_mitochondrial_reads atac_fragments
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 39 24390
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 4 36279
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 26 17979
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 17 8076
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 2 989
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 109 31483
## atac_TSS_fragments
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 7653
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 8887
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 3353
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 1920
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 297
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 7980
## atac_peak_region_fragments
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 7498
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 8372
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 3054
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 1812
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 311
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 7217
## atac_peak_region_cutsites nCount_ATAC
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 13696 13400
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 15050 19199
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 5531 7874
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 3246 4144
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 575 558
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 12965 15159
## nFeature_ATAC nucleosome_signal
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 10783 1.0031188
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 15660 1.2604344
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 7302 1.2748025
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 3953 1.2671301
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 548 0.7471264
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 12405 0.9891261
## nucleosome_percentile TSS.enrichment
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.97 4.966288
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0.99 3.195224
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0.99 3.394106
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0.99 3.581681
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0.62 4.795205
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 0.96 3.463362
## TSS.percentile pct_frags_in_peaks
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.75 30.74211
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0.41 23.07671
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0.42 16.98648
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0.44 22.43685
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0.69 31.44590
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 0.43 22.92348
## percent.mt nCount_SCT nFeature_SCT
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.03342618 4361 1596
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0.02932188 4274 1657
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0.08243371 4407 1629
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0.03766263 4392 1656
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0.03416830 4386 1612
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 0.20590254 4491 1566
## nCount_refAssay nFeature_refAssay
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 89750 9397
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 88671 9644
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 88556 9266
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 87620 9258
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 84874 9106
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 81592 8503
## predicted.class.score predicted.class
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 1 GABAergic
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 1 Glutamatergic
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 1 Glutamatergic
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 1 Glutamatergic
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 1 Glutamatergic
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 1 Glutamatergic
## predicted.cluster.score
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.5815969
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0.4413235
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0.3968808
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0.4890970
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0.9614238
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 0.7664553
## predicted.cluster
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 Inh L5-6 PVALB GAPDHP60
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 Exc L6 THEMIS LINC00343
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 Exc L6 THEMIS LINC00343
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 Exc L6 THEMIS LINC00343
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 Exc L5-6 FEZF2 C9orf135-AS1
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 Exc L6 FEZF2 PROKR2
## predicted.subclass.score
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.6433782
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 1.0000000
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 1.0000000
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 1.0000000
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 1.0000000
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 1.0000000
## predicted.subclass
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 Pvalb
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 L6 IT
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 L6 IT
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 L6 IT
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 L6 CT
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 L6b
## predicted.cross_species_cluster.score
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.5815969
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0.5882976
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0.6879639
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0.5716201
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0.9614238
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 1.0000000
## predicted.cross_species_cluster
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 Pvalb_2
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 L6 IT_1
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 L6 IT_1
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 L6 IT_1
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 L6 CT_2
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 L6b
## mapping.score SCT_snn_res.0.8
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.9985767 12
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0.9994792 10
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0.9986448 10
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0.9979707 10
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0.9997914 10
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 0.9988236 10
## seurat_clusters atac_doublets
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 12 singlet
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 10 singlet
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 10 singlet
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 10 singlet
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 10 singlet
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 10 singlet
## pANN_0.25_0.01_123
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.2745098
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0.3725490
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0.3725490
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0.3529412
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0.4117647
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 0.4313725
## DF.classifications_0.25_0.01_123
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 Singlet
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 Singlet
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 Singlet
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 Singlet
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 Singlet
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 Singlet
## rna_doublets all_doublets region
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 singlet singlet dACC
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 singlet singlet dACC
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 singlet singlet dACC
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 singlet singlet dACC
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 singlet singlet dACC
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 singlet singlet dACC
## pANN_0.25_0.01_493
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_493
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_195
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_195
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_35
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_35
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_184
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_184
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_183
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_183
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_114
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_114
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_126
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_126
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_117
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_117
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_77
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_77
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_209
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_209
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_135
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_135
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_8
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_8
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_201
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_201
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_31
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_31
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_62
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_62
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_68
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_68
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_112
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_112
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_118
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_118
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_61
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_61
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_185
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_185
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_12
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_12
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_295
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_295
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_213
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_213
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_188
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_188
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_39
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_39
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_69
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_69
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_142
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_142
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_413
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_413
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_138
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_138
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## sample
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 1156-Control-dACC
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 1156-Control-dACC
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 1156-Control-dACC
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 1156-Control-dACC
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 1156-Control-dACC
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 1156-Control-dACCdim(obj@meta.data)## [1] 124063 122# 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 nFeature_RNA
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 1156-Control-dACC 89750 9397
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 1156-Control-dACC 88671 9644
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 1156-Control-dACC 88556 9266
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 1156-Control-dACC 87620 9258
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 1156-Control-dACC 84874 9106
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 1156-Control-dACC 81592 8503
## barcode gex_barcode
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 GAGTGATCAGAATGAC-1 GAGTGATCAGAATGAC-1
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 GAGCTGCTCATTCATC-1 GAGCTGCTCATTCATC-1
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 GAAAGGCTCCTTAAGA-1 GAAAGGCTCCTTAAGA-1
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 ATTTAGGTCATGCTAA-1 ATTTAGGTCATGCTAA-1
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 CTCCTCACAGCAATAA-1 CTCCTCACAGCAATAA-1
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 ACGATTCAGCTTCTCA-1 ACGATTCAGCTTCTCA-1
## atac_barcode is_cell excluded_reason
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 ACATTGCGTCTTAGCG-1 1 0
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 TCAAGCGAGACAAGCT-1 1 0
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 GATCAGTAGCCAAACG-1 1 0
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 ATGTCCCAGCTCGACT-1 1 0
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 GTGAACAGTACGTTTA-1 1 0
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 ATGCAAATCTTTAGGT-1 1 0
## gex_raw_reads gex_mapped_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 531010 504121
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 440213 411738
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 478967 451114
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 478048 453252
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 455765 432478
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 436191 415143
## gex_conf_intergenic_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 40409
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 35765
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 37825
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 39712
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 37188
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 31299
## gex_conf_exonic_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 62980
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 68829
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 68563
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 65365
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 71163
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 60555
## gex_conf_intronic_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 363846
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 263836
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 300171
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 315532
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 284694
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 290372
## gex_conf_exonic_unique_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 58101
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 64660
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 63483
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 60576
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 66418
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 56122
## gex_conf_exonic_antisense_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 4622
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 3790
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 4681
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 4447
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 4425
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 4103
## gex_conf_exonic_dup_reads gex_exonic_umis
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 45440 11877
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 48522 15293
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 48439 14106
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 46516 13211
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 51363 14203
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 43648 11812
## gex_conf_intronic_unique_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 337023
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 244322
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 278943
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 292515
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 263862
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 270905
## gex_conf_intronic_antisense_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 20066
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 14859
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 16116
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 17517
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 14384
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 13103
## gex_conf_intronic_dup_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 254687
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 166967
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 199519
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 213638
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 189515
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 197572
## gex_intronic_umis
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 77879
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 73393
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 74472
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 74426
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 70687
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 69814
## gex_conf_txomic_unique_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 54465
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 61779
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 60101
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 57737
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 63376
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 53181
## gex_umis_count gex_genes_count
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0 0
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0 0
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0 0
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0 0
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0 0
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 0 0
## atac_raw_reads atac_unmapped_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 43070 364
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 59998 467
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 30538 213
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 14037 116
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 1717 29
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 55627 450
## atac_lowmapq atac_dup_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 2584 15627
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 3573 19594
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 1982 10270
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 962 4829
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 162 532
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 4374 19082
## atac_chimeric_reads
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 50
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 61
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 34
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 20
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 3
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 85
## atac_mitochondrial_reads atac_fragments
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 39 24390
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 4 36279
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 26 17979
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 17 8076
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 2 989
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 109 31483
## atac_TSS_fragments
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 7653
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 8887
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 3353
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 1920
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 297
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 7980
## atac_peak_region_fragments
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 7498
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 8372
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 3054
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 1812
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 311
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 7217
## atac_peak_region_cutsites nCount_ATAC
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 13696 13400
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 15050 19199
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 5531 7874
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 3246 4144
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 575 558
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 12965 15159
## nFeature_ATAC nucleosome_signal
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 10783 1.0031188
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 15660 1.2604344
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 7302 1.2748025
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 3953 1.2671301
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 548 0.7471264
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 12405 0.9891261
## nucleosome_percentile TSS.enrichment
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.97 4.966288
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0.99 3.195224
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0.99 3.394106
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0.99 3.581681
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0.62 4.795205
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 0.96 3.463362
## TSS.percentile pct_frags_in_peaks
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.75 30.74211
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0.41 23.07671
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0.42 16.98648
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0.44 22.43685
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0.69 31.44590
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 0.43 22.92348
## percent.mt nCount_SCT nFeature_SCT
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.03342618 4361 1596
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0.02932188 4274 1657
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0.08243371 4407 1629
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0.03766263 4392 1656
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0.03416830 4386 1612
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 0.20590254 4491 1566
## nCount_refAssay nFeature_refAssay
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 89750 9397
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 88671 9644
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 88556 9266
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 87620 9258
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 84874 9106
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 81592 8503
## predicted.class.score predicted.class
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 1 GABAergic
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 1 Glutamatergic
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 1 Glutamatergic
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 1 Glutamatergic
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 1 Glutamatergic
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 1 Glutamatergic
## predicted.cluster.score
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.5815969
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0.4413235
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0.3968808
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0.4890970
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0.9614238
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 0.7664553
## predicted.cluster
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 Inh L5-6 PVALB GAPDHP60
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 Exc L6 THEMIS LINC00343
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 Exc L6 THEMIS LINC00343
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 Exc L6 THEMIS LINC00343
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 Exc L5-6 FEZF2 C9orf135-AS1
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 Exc L6 FEZF2 PROKR2
## predicted.subclass.score
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.6433782
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 1.0000000
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 1.0000000
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 1.0000000
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 1.0000000
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 1.0000000
## predicted.subclass
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 Pvalb
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 L6 IT
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 L6 IT
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 L6 IT
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 L6 CT
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 L6b
## predicted.cross_species_cluster.score
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.5815969
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0.5882976
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0.6879639
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0.5716201
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0.9614238
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 1.0000000
## predicted.cross_species_cluster
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 Pvalb_2
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 L6 IT_1
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 L6 IT_1
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 L6 IT_1
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 L6 CT_2
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 L6b
## mapping.score SCT_snn_res.0.8
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.9985767 12
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0.9994792 10
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0.9986448 10
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0.9979707 10
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0.9997914 10
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 0.9988236 10
## seurat_clusters atac_doublets
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 12 singlet
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 10 singlet
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 10 singlet
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 10 singlet
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 10 singlet
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 10 singlet
## pANN_0.25_0.01_123
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 0.2745098
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 0.3725490
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 0.3725490
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 0.3529412
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 0.4117647
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 0.4313725
## DF.classifications_0.25_0.01_123
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 Singlet
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 Singlet
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 Singlet
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 Singlet
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 Singlet
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 Singlet
## rna_doublets all_doublets region.x
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 singlet singlet dACC
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 singlet singlet dACC
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 singlet singlet dACC
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 singlet singlet dACC
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 singlet singlet dACC
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 singlet singlet dACC
## pANN_0.25_0.01_493
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_493
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_195
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_195
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_35
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_35
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_184
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_184
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_183
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_183
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_114
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_114
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_126
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_126
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_117
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_117
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_77
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_77
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_209
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_209
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_135
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_135
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_8
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_8
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_201
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_201
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_31
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_31
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_62
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_62
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_68
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_68
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_112
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_112
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_118
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_118
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_61
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_61
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_185
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_185
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_12
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_12
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_295
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_295
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_213
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_213
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_188
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_188
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_39
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_39
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_69
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_69
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_142
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_142
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_413
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_413
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## pANN_0.25_0.01_138
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 NA
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 NA
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 NA
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 NA
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 NA
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 NA
## DF.classifications_0.25_0.01_138
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 <NA>
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 <NA>
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 <NA>
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 <NA>
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 <NA>
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 <NA>
## sample condition region.y donor
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 1156-Control-dACC Control dACC 1156
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 1156-Control-dACC Control dACC 1156
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 1156-Control-dACC Control dACC 1156
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 1156-Control-dACC Control dACC 1156
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 1156-Control-dACC Control dACC 1156
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 1156-Control-dACC Control dACC 1156
## batch sex age
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 21 Female 53.9
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 21 Female 53.9
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 21 Female 53.9
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 21 Female 53.9
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 21 Female 53.9
## 1156-Control-dACC_ACGATTCAGCTTCTCA-1 21 Female 53.9
## race source
## 1156-Control-dACC_GAGTGATCAGAATGAC-1 Black or African-American Joan
## 1156-Control-dACC_GAGCTGCTCATTCATC-1 Black or African-American Joan
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 Black or African-American Joan
## 1156-Control-dACC_ATTTAGGTCATGCTAA-1 Black or African-American Joan
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 Black or African-American Joan
## 1156-Control-dACC_ACGATTCAGCTTCTCA-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 33524 by 124063## Model formula is y ~ log_umi## Get Negative Binomial regression parameters per gene## Using 2000 genes, 5000 cells## | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100%## Found 74 outliers - those will be ignored in fitting/regularization step## Second step: Get residuals using fitted parameters for 33524 genes## | | | 0% | |= | 1% | |== | 3% | |=== | 4% | |==== | 6% | |===== | 7% | |====== | 9% | |======= | 10% | |======== | 12% | |========= | 13% | |========== | 15% | |=========== | 16% | |============ | 18% | |============= | 19% | |============== | 21% | |=============== | 22% | |================ | 24% | 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|======================================================================| 100%## Calculating gene attributes## Wall clock passed: Time difference of 10.32017 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: LRMDA, DOCK8, ARHGAP24, APBB1IP, ADAM28, AL163541.1, LNCAROD, TBXAS1, FYB1, INPP5D
## P2RY12, PLXDC2, DLEU1, ST6GAL1, SLC1A3, LINC01374, LINC02712, C3, AC008691.1, SLCO2B1
## ARHGAP15, PTPRC, SYK, SLC1A2, RUNX1, ADGRV1, LPAR6, DOCK2, CSF1R, ITPR2
## Negative: KCNIP4, ROBO2, CSMD1, CNTNAP2, RBFOX1, RALYL, SYT1, GRIK1, SNHG14, CNTN5
## ADARB2, DLGAP1, LRRTM4, NXPH1, SGCZ, OPCML, ZNF385D, NRG1, AC011287.1, MEG3
## AC109466.1, KCNQ5, GALNTL6, FGF14, CCSER1, GRIK2, STXBP5L, ATRNL1, DLGAP2, KIAA1217
## PC_ 2
## Positive: LRMDA, DOCK8, APBB1IP, AL163541.1, ADAM28, LNCAROD, ARHGAP24, ST6GAL1, TBXAS1, FYB1
## INPP5D, AC008691.1, P2RY12, LINC01374, LINC02712, KCNIP4, SLCO2B1, C3, ARHGAP15, DLEU1
## PLXDC2, PTPRC, RUNX1, SYK, LPAR6, FRMD4A, DOCK2, CSF1R, ROBO2, CPED1
## Negative: CTNNA3, ST18, RNF220, AC012494.1, MOBP, MBP, AC008571.2, SLC7A14-AS1, AL033523.1, LINC01608
## SLC5A11, PLP1, IL1RAPL1, LINC00609, TF, TMEM144, PCDH9, ENPP2, QKI, KCNH8
## AC079352.1, C10orf90, DOCK5, FRMD4B, SLC24A2, LINC01170, SLC44A1, PIP4K2A, ABCA8, COL4A5
## PC_ 3
## Positive: GPC5, SLC1A2, ADGRV1, OBI1-AS1, AC002429.2, SLC1A3, LINC00499, NKAIN3, HPSE2, DPP10
## AL137139.2, PITPNC1, GPM6A, BMPR1B, SLC4A4, AC012405.1, FAM189A2, GLIS3, NHSL1, LINC00299
## RYR3, RFX4, RANBP3L, CTNNA2, ZNF98, AC114971.1, SLC14A1, GNA14, DTNA, SLCO1C1
## Negative: CTNNA3, ST18, RNF220, MBP, AC012494.1, MOBP, IL1RAPL1, AC008571.2, SLC7A14-AS1, AL033523.1
## LINC01608, SLC5A11, PLP1, FRMD4B, TF, DOCK8, SLC24A2, TMEM144, DOCK10, ENPP2
## KCNH8, APBB1IP, PLXDC2, SLC44A1, C10orf90, LINC01170, PIP4K2A, ABCA8, PLCL1, ELMO1
## PC_ 4
## Positive: LHFPL3, PCDH15, NXPH1, AC004852.2, VCAN, ADARB2, GRIK1, BX284613.2, DSCAM, TNR
## PTPRZ1, SOX6, MEGF11, PDGFRA, LUZP2, KCNMB2, SEMA5A, SGCZ, LRRC4C, SMOC1
## COL9A1, XYLT1, STK32A, CHST11, ERBB4, MIR3681HG, AC124254.2, CA10, ZNF385D, TMEM132C
## Negative: KCNIP4, AC011287.1, RALYL, AC109466.1, AC060765.2, AC034268.2, NRG1, LINC02055, CBLN2, AC073091.3
## IQCJ-SCHIP1, AJ009632.2, AL117329.1, ROBO2, AC008415.1, SYT1, KCNQ5, LINC01090, LDB2, CPNE4
## TAFA1, LINC02306, MEG3, PHACTR1, ADGRV1, DPP10, CELF2, DLGAP2, PTPRD, LINC01378
## PC_ 5
## Positive: ADARB2, ZNF385D, GRIK1, GRIP1, ERBB4, CNTNAP2, NXPH1, RELN, SGCZ, CNTN5
## DLX6-AS1, FSTL5, FGF13, GALNTL6, KCNC2, THSD7B, GAD2, PTCHD4, GRIK2, BTBD11
## AC132803.1, SYNPR, NR2F2-AS1, ROBO2, SLC35F4, PTPRM, ZNF804A, SNHG14, INPP4B, SDK1
## Negative: LHFPL3, KCNIP4, AC004852.2, DSCAM, PCDH15, VCAN, TNR, BX284613.2, CA10, AC011287.1
## PTPRZ1, MEGF11, RALYL, TAFA1, PDGFRA, XYLT1, OPCML, AC060765.2, AC034268.2, CBLN2
## LRRTM4, CSMD1, AL117329.1, LINC02055, MMP16, LRRC4C, PDZRN4, AJ009632.2, SEMA5A, LINC02306ElbowPlot(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
## 349069 features across 124063 samples within 3 assays
## Active assay: ATAC (278944 features, 265036 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
)## 20:00:16 UMAP embedding parameters a = 0.9922 b = 1.112## 20:00:20 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 20
## 20:00:21 3 smooth knn distance failures
## 20:00:24 Initializing from normalized Laplacian + noise (using irlba)
## 20:00:34 Commencing optimization for 200 epochs, with 4069410 positive edges
## 20:01:34 Optimization finished# cluster over neighbor graph
obj <- FindClusters(
object = obj,
algorithm = 4,
resolution = 0.6,
graph.name = 'wsnn',
verbose = TRUE,
method = "igraph"
)## 46 singletons identified. 42 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")
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 converged after 3 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
)## 20:20:53 UMAP embedding parameters a = 0.9922 b = 1.112## 20:20:56 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 20
## 20:20:57 4 smooth knn distance failures
## 20:21:00 Initializing from normalized Laplacian + noise (using irlba)
## 20:21:13 Commencing optimization for 200 epochs, with 4143098 positive edges
## 20:22:18 Optimization finishedAzimuth
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 2215 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 18681 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## 20:26:45 Read 124063 rows## 20:26:45 Processing block 1 of 1## 20:26:45 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 20
## 20:26:45 Initializing by weighted average of neighbor coordinates using 1 thread
## 20:26:46 Commencing optimization for 67 epochs, with 2481260 positive edges
## 20:26:59 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: 1.63210289875666obj_harmony## An object of class Seurat
## 382790 features across 124063 samples within 8 assays
## Active assay: refAssay (33524 features, 2215 variable features)
## 3 layers present: counts, data, scale.data
## 7 other assays present: RNA, ATAC, SCT, prediction.score.class, prediction.score.cluster, prediction.score.subclass, prediction.score.cross_species_cluster
## 8 dimensional reductions calculated: pca, lsi, wnn.umap, harmony_sct_batch, harmony_atac_batch, harm.wnn.umap_batch, integrated_dr, ref.umapDimPlot(obj_harmony, shuffle=TRUE, label = FALSE, repel = TRUE, pt.siz=1,
label.size=0, reduction = "harm.wnn.umap_batch",
group.by = 'predicted.subclass', raster=FALSE) +
theme(legend.text = element_text(size=30),
plot.title = element_text(size=40),
axis.title = element_text(size=30)
)
Leiden clustering
obj_harmony <- FindClusters(
object = obj_harmony,
algorithm = 4,
resolution = 0.6,
graph.name = 'wsnn_batch',
verbose = TRUE,
method = "igraph"
)## 114 singletons identified. 35 final clusters.table(obj_harmony$seurat_clusters)##
## 1 2 3 4 5 6 7 8 9 10 11 12 13
## 17455 17207 11901 9583 8724 6961 6349 4896 4437 3699 3514 3136 3061
## 14 15 16 17 18 19 20 21 22 23 24 25 26
## 3034 2784 2423 2149 1688 1662 1307 1297 1336 1055 796 772 577
## 27 28 29 30 31 32 33 34 35
## 551 502 466 335 258 92 51 3 2head(obj_harmony$seurat_clusters)## 1156-Control-dACC_GAGTGATCAGAATGAC-1 1156-Control-dACC_GAGCTGCTCATTCATC-1
## 15 10
## 1156-Control-dACC_GAAAGGCTCCTTAAGA-1 1156-Control-dACC_ATTTAGGTCATGCTAA-1
## 10 10
## 1156-Control-dACC_CTCCTCACAGCAATAA-1 1156-Control-dACC_ACGATTCAGCTTCTCA-1
## 19 22
## 35 Levels: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 ... 35# sanity check
# https://www.geeksforgeeks.org/check-if-two-objects-are-equal-in-r-programming-setequal-function/
setequal(Idents(obj_harmony), obj_harmony@meta.data$seurat_cluster)## [1] TRUEsetequal(obj_harmony@meta.data$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)
)
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)
)
Assign majority celltype per cluster
df_cluster_celltype <- obj_harmony@meta.data %>%
dplyr::select(seurat_clusters, predicted.subclass) %>%
group_by(seurat_clusters, predicted.subclass) %>%
summarise(n = n()) %>%
top_n(1, n)## `summarise()` has grouped output by 'seurat_clusters'. You can override using
## the `.groups` argument.df_cluster_celltype## # A tibble: 35 × 3
## # Groups: seurat_clusters [35]
## seurat_clusters predicted.subclass n
## <fct> <chr> <int>
## 1 1 Oligo 17452
## 2 2 Oligo 17205
## 3 3 Oligo 11898
## 4 4 Astro 9562
## 5 5 OPC 8698
## 6 6 Micro-PVM 6834
## 7 7 Astro 6271
## 8 8 L2/3 IT 4724
## 9 9 L2/3 IT 4352
## 10 10 L6 IT 1399
## # ℹ 25 more rowsobj_harmony@meta.data$predicted.cell_type_percluster <- plyr::mapvalues(
obj_harmony@meta.data$seurat_clusters,
from = df_cluster_celltype$seurat_clusters,
to = df_cluster_celltype$predicted.subclass)
Idents(obj_harmony) <- "predicted.cell_type_percluster"DimPlot(obj_harmony, shuffle=TRUE, label = TRUE, repel = TRUE, pt.siz=1,
label.size=0, reduction = "harm.wnn.umap_batch",
group.by = 'predicted.cell_type_percluster', raster=FALSE) +
theme(legend.text = element_text(size=30),
plot.title = element_text(size=40),
axis.title = element_text(size=30)
)
Visualize marker genes
DefaultAssay(obj_harmony) <- "SCT"
FeaturePlot(
object = obj_harmony,
features = c("PLP1", # Oligodendrocytes
"AQP4", # Astrocytes
"C1QC", # Microglia
"SV2B", # Excitatory Neurons
"GAD1", # Inhibitory Neurons
"PDGFRA"), # OPCs),
pt.size = 0.2,
label.size = 4,
max.cutoff = 'q95',
ncol = 3,
reduction = "harm.wnn.umap_batch",
label = TRUE,
raster = FALSE,
order = TRUE
)
Save objects
saveRDS(obj_harmony, file = paste0(data_dir, "/", brain_region,
".integrated.batch.analyzed.rds"))
cell_metadata <- obj_harmony@meta.data
saveRDS(cell_metadata, file = paste0(data_dir, "/", brain_region,
".integrated.batch.analyzed.cell_metadata.rds"))Session Info
sessionInfo()## R version 4.2.0 (2022-04-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.6 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/libf77blas.so.3.10.3
## LAPACK: /users/guozy/miniconda3/envs/psych/lib/libopenblasp-r0.3.27.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] RColorBrewer_1.1-3 glue_1.6.2
## [3] data.table_1.14.8 harmony_1.1.0
## [5] Rcpp_1.0.11 BSgenome.Hsapiens.UCSC.hg38_1.4.5
## [7] BSgenome_1.66.3 rtracklayer_1.58.0
## [9] Biostrings_2.66.0 XVector_0.38.0
## [11] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.22.0
## [13] AnnotationFilter_1.22.0 GenomicFeatures_1.50.4
## [15] AnnotationDbi_1.60.2 Biobase_2.58.0
## [17] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
## [19] IRanges_2.32.0 S4Vectors_0.36.2
## [21] BiocGenerics_0.44.0 Azimuth_0.4.6
## [23] shinyBS_0.61.1 Signac_1.9.0
## [25] SeuratObject_5.0.0 Seurat_4.3.0
## [27] viridis_0.6.4 viridisLite_0.4.2
## [29] readr_2.1.4 purrr_1.0.2
## [31] ggplot2_3.5.1 dplyr_1.1.2
## [33] tidyr_1.3.0
##
## loaded via a namespace (and not attached):
## [1] utf8_1.2.4 shinydashboard_0.7.2
## [3] spatstat.explore_3.2-7 reticulate_1.37.0
## [5] tidyselect_1.2.1 RSQLite_2.3.7
## [7] htmlwidgets_1.6.4 grid_4.2.0
## [9] BiocParallel_1.32.6 Rtsne_0.17
## [11] munsell_0.5.1 codetools_0.2-20
## [13] ica_1.0-3 DT_0.33
## [15] future_1.33.2 miniUI_0.1.1.1
## [17] withr_3.0.0 spatstat.random_3.2-3
## [19] colorspace_2.1-0 progressr_0.14.0
## [21] filelock_1.0.3 highr_0.11
## [23] knitr_1.47 ROCR_1.0-11
## [25] tensor_1.5 listenv_0.9.1
## [27] labeling_0.4.3 MatrixGenerics_1.10.0
## [29] GenomeInfoDbData_1.2.9 polyclip_1.10-6
## [31] farver_2.1.2 bit64_4.0.5
## [33] rprojroot_2.0.4 parallelly_1.37.1
## [35] vctrs_0.6.5 generics_0.1.3
## [37] xfun_0.44 BiocFileCache_2.6.1
## [39] R6_2.5.1 humancortexref.SeuratData_1.0.0
## [41] hdf5r_1.3.10 DelayedArray_0.24.0
## [43] bitops_1.0-7 spatstat.utils_3.0-4
## [45] cachem_1.1.0 BiocIO_1.8.0
## [47] promises_1.3.0 scales_1.3.0
## [49] googlesheets4_1.1.1 gtable_0.3.5
## [51] globals_0.16.3 goftest_1.2-3
## [53] spam_2.9-1 rlang_1.1.4
## [55] RcppRoll_0.3.0 splines_4.2.0
## [57] lazyeval_0.2.2 gargle_1.5.2
## [59] spatstat.geom_3.2-9 yaml_2.3.8
## [61] reshape2_1.4.4 abind_1.4-5
## [63] httpuv_1.6.15 SeuratDisk_0.0.0.9021
## [65] tools_4.2.0 SeuratData_0.2.2.9001
## [67] jquerylib_0.1.4 ggridges_0.5.6
## [69] plyr_1.8.9 progress_1.2.3
## [71] zlibbioc_1.44.0 RCurl_1.98-1.14
## [73] prettyunits_1.2.0 deldir_2.0-4
## [75] pbapply_1.7-2 cowplot_1.1.3
## [77] zoo_1.8-12 SummarizedExperiment_1.28.0
## [79] ggrepel_0.9.5 cluster_2.1.6
## [81] here_1.0.1 fs_1.6.4
## [83] magrittr_2.0.3 scattermore_1.2
## [85] lmtest_0.9-40 RANN_2.6.1
## [87] googledrive_2.1.1 ProtGenerics_1.30.0
## [89] fitdistrplus_1.1-11 matrixStats_1.0.0
## [91] hms_1.1.3 patchwork_1.2.0
## [93] shinyjs_2.1.0 mime_0.12
## [95] evaluate_0.24.0 xtable_1.8-4
## [97] RhpcBLASctl_0.23-42 XML_3.99-0.16.1
## [99] gridExtra_2.3 compiler_4.2.0
## [101] biomaRt_2.54.1 tibble_3.2.1
## [103] KernSmooth_2.23-20 crayon_1.5.2
## [105] htmltools_0.5.8.1 later_1.3.2
## [107] tzdb_0.4.0 DBI_1.2.3
## [109] dbplyr_2.5.0 MASS_7.3-56
## [111] rappdirs_0.3.3 Matrix_1.6-1.1
## [113] cli_3.6.2 parallel_4.2.0
## [115] dotCall64_1.1-1 igraph_2.0.3
## [117] pkgconfig_2.0.3 GenomicAlignments_1.34.1
## [119] sp_2.1-4 plotly_4.10.4
## [121] spatstat.sparse_3.0-3 xml2_1.3.6
## [123] bslib_0.7.0 stringr_1.5.1
## [125] digest_0.6.35 sctransform_0.4.0
## [127] RcppAnnoy_0.0.22 spatstat.data_3.0-4
## [129] rmarkdown_2.27 cellranger_1.1.0
## [131] leiden_0.4.3.1 fastmatch_1.1-4
## [133] uwot_0.2.2 restfulr_0.0.15
## [135] curl_5.2.1 shiny_1.8.1.1
## [137] Rsamtools_2.14.0 rjson_0.2.21
## [139] lifecycle_1.0.4 nlme_3.1-164
## [141] jsonlite_1.8.8 fansi_1.0.6
## [143] pillar_1.9.0 lattice_0.22-6
## [145] KEGGREST_1.38.0 fastmap_1.2.0
## [147] httr_1.4.7 survival_3.6-4
## [149] png_0.1-8 bit_4.0.5
## [151] presto_1.0.0 stringi_1.8.4
## [153] sass_0.4.9 blob_1.2.4
## [155] memoise_2.0.1 irlba_2.3.5.1
## [157] future.apply_1.11.2