ctcr.md

title	2019 TCGA Conference and Workshop in India
link
image

Starting Docker instructions

• docker pull tiagochst/elmer_jupterhub:notebooks_data
• docker run -p 3838:3838 -d --name jupyterhub tiagochst/elmer_jupterhub:notebooks_data jupyterhub --ip 0.0.0.0 --port 3838
• Open http://localhost:3838 in browser (user:student1 pass:student1)
• docker stop $(docker ps -q)
• docker rm $(docker ps -a -q)

R markdown

• TCGA data analysis (RPubs version)
• Creating MAE Objects
• ELMER (reduced RAM)
• ELMER
• ATAC-seq

Papers

• R_TCGABiolinks_NAR_2016.pdf
• R_MultiAssayExperiment_CancerResearch_2017.pdf
• GENOMIC_Maftools_GenomeRes_2018.pdf
• EPIGENETICS_ELMER_Bioinformatics_2019.pdf
• EPIGENETICS_ATACseq_Science_2018.pdf

Molecular subtypes (TCGABiolinks)

• Synapse
• Google Doc