Resources for TCGA data mining

Data sources

The Cancer Genome Atlas

• Overview
• Data Portal
• Legacy Data Portal

Working with TCGA barcodes

• TCGA Barcodes

GDAC Broad Firehose

• GDAC Firehose
• GDAC Firebrowse

Example expression dataset retrieval for ACC:

# ACC RSEM genes normalized
wget http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/ACC/20160128/gdac.broadinstitute.org_ACC.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2016012800.0.0.tar.gz

tar xzvf gdac.broadinstitute.org_ACC.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2016012800.0.0.tar.gz

head gdac.broadinstitute.org_ACC.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2016012800.0.0/ACC.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data.txt

Good practices

Reproducibility and transparency

• Good enough practices in scientific computing (Wilson et al.)
• The extent and consequences of p-hacking in science (Head et al.)

Version control

• Git manual (short)
• A Quick Introduction to Version Control with Git and GitHub (Blischak et al.)
• Github
• Bitbucket

Literate programing

• Rmarkdown (R)
• Python notebooks

Code styling

• Google’s R style guide
• Python PEP8

Training

• SIB Swiss Institute of Bioinformatics tutorial on UNIX
• Shell cheatsheet
• awk cheatsheet

Slack channel

• Pancancer Epigenomics Slack channel

Last updated 15th Jan 2019 by imallona

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