{"name":"brca/brca_promoter.probeMap","type":"probeMap","version":"2018-07-04","wrangling_procedure":"Promoter is defined as peak summit within -1000 to 100bp from TSS sites.","url":"https://www.synapse.org/#!Synapse:syn12578198","assembly":"hg38"}

{"cohort":"GDC TCGA Breast Cancer (BRCA)","url":"https://gdc.cancer.gov/about-data/publications/ATACseq-AWG","probeMap":"brca/brca_promoter.probeMap","dataSubType":"ATAC-seq","label":"promoter peak signal","name":"brca/brca_peak_Log2Counts_dedup_promoter","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 file brca_peak_Log2Counts_dedup_promoter. <br>Promoters are defined as in -1000 to 100bp from a gene's TSS sites. Promoter peaks are those peaks whose summit locates in the promoter region. Peak location is from file BRCA.fwp.filter.non_overlapping.annotated.rds.","type":"genomicMatrix","version":"2018-07-05","unit":"log2((count+5)PM)-qn","colnormalization":true}

{"name":"brca/pam50","cohort":"GDC TCGA Breast Cancer (BRCA)","dataSubType":"phenotype","label":"pam50 subtype","type":"clinicalMatrix","clinicalfeature":"brca/clinFeature","version":"2018-07-05"}

{"name":"brca/elmer.all.pairs.significant.probeMap","type":"probeMap","version":"2018-07-06","wrangling_procedure":"download BRCA_supervised_analaysis_molecular_subtypes_hg38_may_7.zip and BRCA_unsupervised_hg38.zip from synapse. Use all files getPair.*.pairs.significant.csv to generate probe to gene mapping","url":"https://www.synapse.org/#!Synapse:syn12664787, https://www.synapse.org/#!Synapse:syn12664793","assembly":"hg38"}