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links.txt
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# 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