# R binaries ----------- https://atrev.s3.amazonaws.com/brainchromatin/AllGenes_GenomicRanges.RDS https://atrev.s3.amazonaws.com/brainchromatin/CCA_Matching.RDS https://atrev.s3.amazonaws.com/brainchromatin/GA_RNA_Correlations.RDS https://atrev.s3.amazonaws.com/brainchromatin/Matrix_Glial_KNNpseudoBulk_ATAC_Accessibility.RDS https://atrev.s3.amazonaws.com/brainchromatin/Matrix_Glial_KNNpseudoBulk_ATAC_ChromVAR.RDS https://atrev.s3.amazonaws.com/brainchromatin/Matrix_Glial_KNNpseudoBulk_ATAC_GeneActivity.RDS https://atrev.s3.amazonaws.com/brainchromatin/Matrix_Glial_KNNpseudoBulk_RNA_Full.RDS https://atrev.s3.amazonaws.com/brainchromatin/PeakGeneLinks_All.RDS https://atrev.s3.amazonaws.com/brainchromatin/PeakGeneLinks_Significant.RDS https://atrev.s3.amazonaws.com/brainchromatin/RNA_GlialPseudobulks.RDS https://atrev.s3.amazonaws.com/brainchromatin/SamplePseudoBulk_Glial_KNNpseudobulk_ATAC_GA.RDS https://atrev.s3.amazonaws.com/brainchromatin/FCM_Object.RDS https://atrev.s3.amazonaws.com/brainchromatin/scATAC_Colors.txt # (Color scheme) https://atrev.s3.amazonaws.com/brainchromatin/scATAC_ChromVAR_SCE.RDS https://atrev.s3.amazonaws.com/brainchromatin/scATAC_GeneActivity.RDS https://atrev.s3.amazonaws.com/brainchromatin/scATAC_MotifMatchMatrix.RDS https://atrev.s3.amazonaws.com/brainchromatin/scATAC_SCE.RDS https://atrev.s3.amazonaws.com/brainchromatin/scRNA_Cluster_Markers.RDS https://atrev.s3.amazonaws.com/brainchromatin/scRNA_Colors.txt https://atrev.s3.amazonaws.com/brainchromatin/scRNA_SCE2.RDS https://atrev.s3.amazonaws.com/brainchromatin/scRNA_URD_GlialCells.RDS https://atrev.s3.amazonaws.com/brainchromatin/TF_MotifExpressionCorrelation.RDS https://atrev.s3.amazonaws.com/brainchromatin/Multiome_RNA_SCE.RDS https://atrev.s3.amazonaws.com/brainchromatin/Multiome_ATAC_SCE.RDS https://atrev.s3.amazonaws.com/brainchromatin/Multiome_ATAC_GeneActivity.RDS https://atrev.s3.amazonaws.com/brainchromatin/scRNA_Seurat.RDS # Processed Data Files: Counts, peaks, links, ChromVAR, and cell metadata ------- # -- ATAC https://atrev.s3.amazonaws.com/brainchromatin/atac_cell_metadata.txt https://atrev.s3.amazonaws.com/brainchromatin/atac_chromVAR_TF_activities.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/atac_consensus_peaks.bed.gz https://atrev.s3.amazonaws.com/brainchromatin/atac_counts.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/atac_gene_activities.tsv.gz # -- RNA https://atrev.s3.amazonaws.com/brainchromatin/peak_gene_links.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/rna_cell_metadata.txt https://atrev.s3.amazonaws.com/brainchromatin/velo_colData.txt https://atrev.s3.amazonaws.com/brainchromatin/rna_cell_names.txt https://atrev.s3.amazonaws.com/brainchromatin/rna_counts.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/umapModel_rna_hft_uwot # -- Multiome # RNA https://atrev.s3.amazonaws.com/brainchromatin/multiome_cell_metadata.txt https://atrev.s3.amazonaws.com/brainchromatin/multiome_cluster_names.txt https://atrev.s3.amazonaws.com/brainchromatin/multiome_rna_counts.tsv https://atrev.s3.amazonaws.com/brainchromatin/multiome_spliced_rna_counts.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/multiome_unspliced_rna_counts.tsv.gz # ATAC https://atrev.s3.amazonaws.com/brainchromatin/multiome_atac_consensus_peaks.txt.gz https://atrev.s3.amazonaws.com/brainchromatin/multiome_atac_gene_activities.tsv https://atrev.s3.amazonaws.com/brainchromatin/multiome_atac_counts.tsv.gz # ATAC cluster-specific BigWigs --------------- # Used to train ATAC-seq models https://atrev.s3.amazonaws.com/brainchromatin/hft_c0.bw https://atrev.s3.amazonaws.com/brainchromatin/hft_c10.bw https://atrev.s3.amazonaws.com/brainchromatin/hft_c11.bw https://atrev.s3.amazonaws.com/brainchromatin/hft_c13.bw https://atrev.s3.amazonaws.com/brainchromatin/hft_c14.bw https://atrev.s3.amazonaws.com/brainchromatin/hft_c15.bw https://atrev.s3.amazonaws.com/brainchromatin/hft_c1.bw https://atrev.s3.amazonaws.com/brainchromatin/hft_c2.bw https://atrev.s3.amazonaws.com/brainchromatin/hft_c3.bw https://atrev.s3.amazonaws.com/brainchromatin/hft_c4.bw https://atrev.s3.amazonaws.com/brainchromatin/hft_c5.bw https://atrev.s3.amazonaws.com/brainchromatin/hft_c6.bw https://atrev.s3.amazonaws.com/brainchromatin/hft_c7.bw https://atrev.s3.amazonaws.com/brainchromatin/hft_c8.bw https://atrev.s3.amazonaws.com/brainchromatin/hft_c9.bw # Singleome ATAC Fragments Files ---------- # -- Singleome https://atrev.s3.amazonaws.com/brainchromatin/hft_w16_p7_r1_fragments.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/hft_w16_p7_r1_fragments.tsv.gz.tbi https://atrev.s3.amazonaws.com/brainchromatin/hft_w16_p7_r2_fragments.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/hft_w16_p7_r2_fragments.tsv.gz.tbi https://atrev.s3.amazonaws.com/brainchromatin/hft_w16_p7_r3_fragments.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/hft_w16_p7_r3_fragments.tsv.gz.tbi https://atrev.s3.amazonaws.com/brainchromatin/hft_w20_p3_r1_fragments.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/hft_w20_p3_r1_fragments.tsv.gz.tbi https://atrev.s3.amazonaws.com/brainchromatin/hft_w20_p3_r2_fragments.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/hft_w20_p3_r2_fragments.tsv.gz.tbi https://atrev.s3.amazonaws.com/brainchromatin/hft_w21_p5_r1_fragments.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/hft_w21_p5_r1_fragments.tsv.gz.tbi https://atrev.s3.amazonaws.com/brainchromatin/hft_w21_p5_r2_fragments.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/hft_w21_p5_r2_fragments.tsv.gz.tbi https://atrev.s3.amazonaws.com/brainchromatin/hft_w21_p5_r3_fragments.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/hft_w21_p5_r3_fragments.tsv.gz.tbi https://atrev.s3.amazonaws.com/brainchromatin/hft_w21_p5_r4_fragments.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/hft_w21_p5_r4_fragments.tsv.gz.tbi https://atrev.s3.amazonaws.com/brainchromatin/hft_w24_p6_r1_fragments.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/hft_w24_p6_r1_fragments.tsv.gz.tbi https://atrev.s3.amazonaws.com/brainchromatin/hft_w24_p6_r2_fragments.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/hft_w24_p6_r2_fragments.tsv.gz.tbi https://atrev.s3.amazonaws.com/brainchromatin/hft_w24_p6_r3_fragments.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/hft_w24_p6_r3_fragments.tsv.gz.tbi https://atrev.s3.amazonaws.com/brainchromatin/hft_w24_p6_r4_fragments.tsv.gz https://atrev.s3.amazonaws.com/brainchromatin/hft_w24_p6_r4_fragments.tsv.gz.tbi # ---- Multiome CellRanger output # -- Prefixes # https://atrev.s3.amazonaws.com/brainchromatin/hft_ctx_w21_dc1r3_r1/outs/* # https://atrev.s3.amazonaws.com/brainchromatin/hft_ctx_w21_dc2r2_r1/outs/* # https://atrev.s3.amazonaws.com/brainchromatin/hft_ctx_w21_dc2r2_r2/outs/* # -- Suffixes (BAM files have been removed) # atac_cut_sites.bigwig # atac_fragments.tsv.gz # atac_fragments.tsv.gz.tbi # atac_peak_annotation.tsv # atac_peaks.bed # filtered_feature_bc_matrix.h5 # filtered_feature_bc_matrix/barcodes.tsv.gz # filtered_feature_bc_matrix/features.tsv.gz # filtered_feature_bc_matrix/matrix.mtx.gz # per_barcode_metrics.csv # raw_feature_bc_matrix.h5 # raw_feature_bc_matrix/barcodes.tsv.gz # raw_feature_bc_matrix/features.tsv.gz # raw_feature_bc_matrix/matrix.mtx.gz # summary.csv