{"name":"TCGA_ATAC_peak.all.probeMap","type":"probeMap","assembly":"hg38","wrangling_procedure":"map peaks to all genes within 500kb on each side of the peak summit","url":"https://www.synapse.org/#!Synapse:syn12511521","version":"2018-08-01"}

{"cohort":"GDC Pan-Cancer (PANCAN)","url":"https://gdc.cancer.gov/about-data/publications/ATACseq-AWG","probeMap":"TCGA_ATAC_peak.all.probeMap","dataSubType":"ATAC-seq","label":"All peak signal","name":"TCGA_ATAC_peak_Log2Counts_dedup_sample","wrangling_procedure":"Normalized count matrix: a prior count of 5 is added to the raw counts, then put into a \"counts per million\", then log2 transformed, then quantile normalized, the result is TCGA_ATAC_Log2Counts_Matrix.180608.txt.gz.  We downloaded TCGA_ATAC_Log2Counts_Matrix.180608.txt.gz from synapse, averaged the values in the file (i.e. log2((count+5)PM)-qn values) across all technical replicates and all biospecimens belong to the same TCGA sample. The result is the genomic matrix TCGA_ATAC_peak_Log2Counts_dedup_sample. Peak location information is from file TCGA_ATAC_Log2Counts_Matrix.180608.txt.gz. Peak to gene mapping is defined as all peaks whose summit locates within 500kb from a gene's TSS sites.","type":"genomicMatrix","version":"2018-06-21","unit":"log2((count+5)PM)-qn"}

{"name":"TCGA_ATAC_peak.Linkage.probeMap","type":"probeMap","version":"2018-06-25","wrangling_procedure":"convert ATAC_Peak_Linkage.txt enhancerID to TCGA_ATAC_Log2Counts_Matrix.180608.txt peak ids, then format to xena probeMap","url":"https://www.synapse.org/#!Synapse:syn12510147","assembly":"hg38"}

{"cohort":"GDC Pan-Cancer (PANCAN)","url":"https://gdc.cancer.gov/about-data/publications/ATACseq-AWG","probeMap":"TCGA_ATAC_peak.Linkage.probeMap","dataSubType":"ATAC-seq","label":"Enhancer peak signal","name":"TCGA_ATAC_peak_Log2Counts_dedup_sample_hQlinkage","wrangling_procedure":"Normalized count matrix: a prior count of 5 is added to the raw counts, then put into a \"counts per million\", then log2 transformed, then quantile normalized, the result is TCGA_ATAC_Log2Counts_Matrix.180608.txt.gz.  We download TCGA_ATAC_Log2Counts_Matrix.180608.txt.gz from synapse, average the values in the file (i.e. log2((count+5)PM)-qn values) across all technical replicates and all biospecimens belong to the same TCGA sample. The result is the genomic matrix TCGA_ATAC_peak_Log2Counts_dedup_sample_hQlinkage.<br>The peak to gene mapping is the predicted peak-gene links, excluded promoters to be conservative. The mapping information is downloaded from https://gdc.cancer.gov/about-data/publications/ATACseq-AWG.","type":"genomicMatrix","version":"2018-06-25","unit":"log2((count+5)PM)-qn","colnormalization":true}