Hello to everyone!
I have built CRAN task view for genetics. For now I have not submit it
to CRAN yet and it can be accessible from:
http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.html
http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.ctv
I have not submitted it to CRAN, since I would like first some opinion
about it. Genetics is really so broad field that I belive one person can
not know about every corner. So I would like to get some suggestions,
crtitics, pacthes to presentation from my knowledge limited point view.
Please note that field of microarray/proteomics, ... area is
substantially supported in R and Bioconductor and if someone is prepaired
to write a CRAN task view for this I can remove that piece text from my
view and provide a link.
I have sent this mail also to all mentioned/listed package maintainers.
Lep pozdrav / With regards,
Gregor Gorjanc
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University of Ljubljana
Biotechnical Faculty URI: http://www.bfro.uni-lj.si/MR/ggorjan
Zootechnical Department mail: gregor.gorjanc <at> bfro.uni-lj.si
Groblje 3 tel: +386 (0)1 72 17 861
SI-1230 Domzale fax: +386 (0)1 72 17 888
Slovenia, Europe
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"One must learn by doing the thing; for though you think you know it,
you have no certainty until you try." Sophocles ~ 450 B.C.
Dear Gorjanc, It is a good idea to make an CTV for genetics. I made an informal summary to Hum Genomics a short while ago and quoted below. ... some packages for genetic data analysis, which fall into several categories: basic data manipulation (genetics) phylogenetic analysis (PHYLOGR, ape), association analysis of population including population structure (genetics, hapassoc, haplo.score, haplo.stats, hierfstat, hwde, ldDesign, LDheatmap, Malmig, popgen, R/gap, rmetasim) and family data (tdthap), QTL for experimental design (bim, bqtl, qtlDesign, R/qtl). Others (BradleyTerry, epitools, evd, gllm, locfdr, rmeta, vcd) are quite general. It missed out biodemo but actually included kinship. Further it appears seao is not that genetics as it is quite general. Also note that the genetics package needs packages such as combinat and gregmisc. BW Jing Hua [[alternative HTML version deleted]]
Hi Gregor, The compiled list of genetics packages is a great idea, I'll certainly find it useful as it took me quite some time to track them all down through CRAN. I've a couple of things that could be added... qvalue - A procedure for false discovery rate control. General, but developed for the general area of genetics (see Sotrey & Tibshirani 2003 PNAS 100:9440-9445) SimHap - still in development (Beta testing), this is a Java GUI front end for performing a range of statistical genetics analyses, very useful for occasional users who can not get their heads round CLI's. Registration with the author is currently required. Regards Neil -- Neil Shephard Genetics Statistician, ARC Epidemiology Unit neil.shephard at manchester.ac.uk nshephard at gmail.com