i0biods14 => #biodata14
i0pcawg14 => i0pcawg14+exrna
https://storify.com/markgerstein/favorite-tweets-from-biological-data-science-i0bio
https://linkstream2.gerstein.info/tag/i0pcawg14
https://linkstream2.gerstein.info/tag/i0biods14
http://lectures.gersteinlab.org/summary/nc-annotation-sect-from–PAWG-2-5-9-14_prep_for_Boston_mtg
– how to expand beyond 12 tumors?
– reclassification of lung squam. lung adeno. & subdivisions of breast cancer
Hoadley et al. … Stuart
http://www.sciencedirect.com/science/article/pii/S0092867414008769?via=ihub
“mutsig2CV”
MutSig – 1.0 – Getz et al. Science 2007
MutSigCV – CV – covariates
mutations need to cluster at hotspots & in functional regions
http://www.sciencemag.org/content/317/5844/1500.2
Science 14 September 2007:
Vol. 317 no. 5844 p. 1500
DOI: 10.1126/science.1138764
TECHNICAL COMMENTS
Comment on “The Consensus Coding Sequences of Human Breast and Colorectal Cancers”
Gad Getz1,*,†,
Holger Höfling2,*,
Jill P. Mesirov1,
Todd R. Golub1,3,4,5,6,
Matthew Meyerson1,3,
Robert Tibshirani2,7,
Eric S. Lander1,6,8
Nice heatmap tool
http://www.gitools.org/home
contains a mechanisms pipeline, similar to breakseq
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3704973/#!po=42.5926
Cell. Author manuscript; available in PMC May 9, 2014.
Cell. May 9, 2013; 153(4): 919–929.
doi: 10.1016/j.cell.2013.04.010
PMCID: PMC3704973
NIHMSID: NIHMS475485
Diverse mechanisms of somatic structural variations in human cancer genomes Lixing Yang,1 Lovelace J. Luquette,1 Nils Gehlenborg,1,2 Ruibin Xi,1 Psalm S. Haseley,1,3 Chih-Heng Hsieh,4Chengsheng Zhang,4 Xiaojia Ren,3 Alexei Protopopov,5 Lynda Chin,5 Raju Kucherlapati,3,6 Charles Lee,4 and Peter J. Park1,3,7,*
