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leekgroup / derfinder

R package for DER Finder, a method for differential expression analysis of RNA-seq data
http://biostatistics.oxfordjournals.org/content/early/2014/01/06/biostatistics.kxt053.short?rss=1
MIT License
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package locfdr was removed from CRAN #9

Closed brianhigh closed 9 years ago

brianhigh commented 9 years ago

In your README.md, you mention locfdr in the installation section. Since locfdr has been removed from CRAN, you might want to use an alternative which is still supported. Some suggestions may be found in this stackoverflow thread. The packages twilight and fdrtool were suggested and some examples were given in that thread. Otherwise a archived package for locfdr must be used, as in...

library(devtools)
install_url("http://cran.r-project.org/src/contrib/Archive/locfdr/locfdr_1.1-7.tar.gz")
lcolladotor commented 9 years ago

Yes, you need to use an archived version of locfdr. As @alyssafrazee has said, this version is no longer maintained.

I added more detail on the installation instructions with https://github.com/alyssafrazee/derfinder/pull/14

brianhigh commented 9 years ago

I tried today with R 2.15.x and this issue does not come up with R 2.15.3. So, this issue can be closed.