Hi again, On Mon, Mar 23, 2020 at 09:19:09PM +0100, Andreas Tille wrote: > Hi Pranav, > > On Mon, Mar 23, 2020 at 09:24:17PM +0530, Pranav Ballaney wrote: > > Hi Andreas, > > I shared the email thread about the biohackathon with a friend of mine, > > Shruti Sridhar, and she has put together the following list. > > It would be great if your friend Shruti Sridhar would subscribe > > https://lists.debian.org/debian-med > > > 1) chipseq - ChIP-Seq analysis - PscanCHIP is there but that is only to > > identify transcription sites > > Just injected into salsa (not a finalised package but sufficient > metadata to create a sensible entry on the tasks page after the next 24 > hours). > > > 2) Rcpi - drug discovery > > 3) Mediana - I saw rpact this is kinda similar but better for survival > > analysis in clinical trials > > 4) So there is this package in R called TCGAbiolinks - I'm sure there will > > be an equivalent for it in Debain but there are several databses like TCGA > > that need integration > > 5) GSEPD - its a new Bioconductor package that nicely brings together > > DESeq2 and GOSeq functions > > 6) PWMEnrich and motifstack - denovo motif analysis - I think this will be > > useful for even the Covid tag that is there > > 7) MutationalPatterns - this allows to detect patterns in base subtituions > > ( really cool for Covid) also there is one more called > > CancerMutationAnalysis which will be useful for the Oncology tag > > > > > > I've included links to the sources here: > > This is extremely valuable input. Thanks a lot. I'll keep on > adding rough packaging metadata to kickstart packaging. > > Any further help of this kind is very welcome. Thanks a lot > > Andreas. > > > [1] https://ccg.epfl.ch//chipseq/ > > [2] https://github.com/nanxstats/Rcpi > > [3] https://github.com/gpaux/Mediana > > [4] https://github.com/BioinformaticsFMRP/TCGAbiolinks
(At least) 2-4 are on CRAN or BioConductor. That's extremely simple packaging. Most of this is automated. The bad news is that TCGAbiolinks depends from locfit. We are discussing with CRAN maintainers that locfit is non-distributable and should be removed from CRAN. This is extremely important and should happen soon to make upstream authors aware not to use that CRAN package. Rcpi needs some preconditions (also automatically created) but these should be OK and may be I get it in the next couple of days to new. The ones below also are "smelling" like R packages. :-) Thanks again for your hints, Andreas. > > [5] https://github.com/kstammits/rgsepd > > [6] http://bioconductor.org/packages/release/bioc/html/PWMEnrich.html and > > https://github.com/jianhong/motifStack > > [7] https://github.com/UMCUGenetics/MutationalPatterns > > > > Please take a look and let me know if they can be added to the task list. > > > > Regards, > > Pranav > > > > ᐧ > > -- > http://fam-tille.de -- http://fam-tille.de
