Notes from the BoF Bioc2017 Discussions Courtesy of moderator Sonali Arora
This repository contains a brief outline for a "Birds-of-Feather" (BOF) session to meet and discuss analyzing publicly available cancer data from TCGA & GTEx
29 primary sites
Sources for getting TCGA data
Nice interactive way of choosing samples, create a manifest file , and then download using gdc data transfer tool.
+ data is made available as a Bioconductor RangedSummarizedExperiment object.
+ data from select publications is also available
+ gene level and exon level data is present.
contains data from other sources too such as ICGC, TARGET, GTEx , TOIL
RNASeq data is present as log2(RPKM+1),no raw read counts to use as input for edgeR or DESeq2
mutation data, copy number data, protein expression RRPA, DNA methylation, miRNA isoform expression data.
ExperimentHub() contains raw RNASeq gene counts from TCGA. GSE62944
eh = ExperimentHub()
tumor_samples = eh[["EH164"]]
normal_sample = eh[["EH165"]]
- Re-normalize RNASeq data from TCGA using kallisto can be found here
Sources for getting GTEx data
Coming Soon!! will be added to ExperimentHub()
What kind of analysis do you typically do with TCGA/GTEx data ? Packages being used ?
clustering of samples/ genes - PCA plots.
differenrial expression analysis between 2 chosen groups?0 using RNASeq data
Other publicly available databases for Cancer / Cool resources for studying cancer
Martin Morgan & the Core Bioconductor Team
GTEx Project - The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. The data used for the analyses described in this manuscript were obtained from: [insert, where appropriate] the GTEx Portal on MM/DD/YY and/or dbGaP accession number phs000424.vN.pN on MM/DD/YYYY.
TCGA data discussed here is generated by the TCGA Research Network: http://cancergenome.nih.gov/.