{"cohort":"GDC Pan-Cancer (PANCAN)","min":0,"url":"http://zwdzwd.github.io/pmd.html","probeMap":"WGBS/coord_uniq_sorted_probemap","dataSubType":"DNA methylation","label":"WGBS CpG site signal","max":1,"name":"WGBS/tcga.WGBS.xena","type":"genomicMatrix","version":"2018-07-19","unit":"beta value"}

{"name":"brca/brca_peak.probeMap","type":"probeMap","assembly":"hg38","wrangling_procedure":"peaks summit within 500kb of TSS sites","version":"018-07-04","url":"https://www.synapse.org/#!Synapse:syn12578198"}

{"cohort":"GDC TCGA Breast Cancer (BRCA)","url":"https://gdc.cancer.gov/about-data/publications/ATACseq-AWG","probeMap":"brca/brca_peak.probeMap","dataSubType":"ATAC-seq","label":"All peak signal","name":"brca/brca_peak_Log2Counts_dedup","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 embedded in the file BRCA.fwp.filter.non_overlapping.annotated.rds. We downloaded BRCA.fwp.filter.non_overlapping.annotated.rds 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 brca_peak_Log2Counts_dedup. Peak location information is from file BRCA.fwp.filter.non_overlapping.annotated.rds. Peak to gene mapping is defined as any peak summit locates within 500kp from a gene's TSS sites.","type":"genomicMatrix","version":"2018-07-04","unit":"log2((count+5)PM)-qn"}

{"cohort":"GDC TCGA Breast Cancer (BRCA)","url":"https://gdc.cancer.gov/about-data/publications/ATACseq-AWG","probeMap":"brca/brca_enhencer.probeMap","dataSubType":"ATAC-seq","label":"enhancer peak signal","name":"brca/brca_peak_Log2Counts_dedup_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 embedded in the file BRCA.fwp.filter.non_overlapping.annotated.rds. We downloaded BRCA.fwp.filter.non_overlapping.annotated.rds from synapse, averaged the values in the file (i.e. log2(count+5)-qn values) across all technical replicates and all biospecimens belong to the same TCGA sample. The result is the genomic matrix file brca_peak_Log2Counts_dedup_hQlinkage.<br>Peak locations are from file BRCA.fwp.filter.non_overlapping.annotated.rds. Enhancer peak to gene linkage is from https://gdc.cancer.gov/about-data/publications/ATACseq-AWG. The peak to gene mapping is the predicted peak-gene links, excluded promoters to be conservative.","type":"genomicMatrix","version":"2018-07-04","unit":"log2((count+5)PM)-qn","colnormalization":true}