[Bioc-devel] new package: canceR
kmezhoud at gmail.com
Thu Mar 26 20:49:54 CET 2015
I am pleased to announce the release of new package named canceR
main goal of this package is to facilitate to NOT R user the access of
complex cancer genomics data hosted by the MSKCC and available through
cgdsr CRAN package. By simple clic, the user can combine Cases (Samples)
and Genetic profiles to get rapidly without programming skills all
available cancer genomics data (CNA, mRNA, Methylation, Mutation, miRNA,
RPPA) in exportable table.
Compared to cBioportal <http://www.cbioportal.org/>, canceR allows user to
focus on some Studies and get specific data as Amino Acid changes in
Mutation Data for selected gene list.
The second part of canceR focus on modeling. I selected some interesting
fonctions from others packages (see Vignette) and I adapted them to
1-Associate phenotypes (gene / variable ) to disease
2-Classify genes by phenotype or disease
3-Enrichment gene expression data using GSEA-R (Broad Institute)
Other function is in progress to facilitated the visualization of multi
Dimensional Genomics Data for multiples cancers using Circos styles.
Please fill free for any suggestions.
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