https://github.com/bhklab/metagx
Scripts to perform meta-analysis of cancer gene expression datasets
https://github.com/bhklab/metagx
gene-expression meta-analysis
Last synced: about 2 months ago
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Scripts to perform meta-analysis of cancer gene expression datasets
- Host: GitHub
- URL: https://github.com/bhklab/metagx
- Owner: bhklab
- Created: 2015-01-08T22:43:37.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2018-03-26T22:38:00.000Z (about 7 years ago)
- Last Synced: 2025-03-27T14:04:24.847Z (2 months ago)
- Topics: gene-expression, meta-analysis
- Language: R
- Homepage:
- Size: 12.5 MB
- Stars: 7
- Watchers: 26
- Forks: 8
- Open Issues: 5
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Metadata Files:
- Readme: README.md
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README
MetaGx
=======
Scripts to perform meta-analysis of cancer gene expression datasets
Dependencies:
Install the R/Bioconductior dependencies:
pp <- c("Biobase", "BiocGenerics", "org.Hs.eg.db", "survival", "survcomp", "genefu", "mRMRe", "WriteXLS")
source("http://bioconductor.org/biocLite.R")
myrepos <- biocinstallRepos()
rr <- biocLite(pkgs=pp, dependencies=TRUE, type="source", destdir=".")
If using Windows:
- WriteXLS needs Perl to be installed. To check if perl has been installed:
library(WriteXLS)
testPerl(perl="perl", verbose=TRUE)
TODO
- Adapt the package to handle curatedOvarianData
- Weighted survival does not work properly (number of patients per time points should be "unweighted")