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Revision 13 as of 2009-03-16 03:32:12
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||Hapoltyping||[http://www.biostat.umn.edu/~nali/SoftwareListing.html Hotspotter]||no licence||did not build out of the box on ppc|| ||no||
||Association studies||[http://claire.bardel.free.fr/software.html altree]||as Perl itself||unofficial ([http://dept-info.labri.fr/~danjean/deb.html#altree ens-lyon])||free||no||
||Linkage desequilibrium studies||[http://www.genome.mcgill.ca/~mlemire/software.html SUP]||GPL||Depends on FastSLINK||free||no||
||QTL / SNP analysis||[http://www.well.ox.ac.uk/happy/happyR.shtml happy]||[http://www.well.ox.ac.uk/happy/disclaimer.shtml free]||R package||free||no||
||Hapoltyping||[[http://www.biostat.umn.edu/~nali/SoftwareListing.html|Hotspotter]]||no licence||did not build out of the box on ppc|| ||no||
||Association studies||[[http://claire.bardel.free.fr/software.html|altree]]||as Perl itself||unofficial ([[http://dept-info.labri.fr/~danjean/deb.html#altree|ens-lyon]])||free||no||
||Linkage desequilibrium studies||[[http://www.genome.mcgill.ca/~mlemire/software.html|SUP]]||GPL||Depends on FastSLINK||free||no||
||QTL / SNP analysis||[[http://www.well.ox.ac.uk/happy/happyR.shtml|happy]]||[[http://www.well.ox.ac.uk/happy/disclaimer.shtml|free]]||R package||free||no||
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||QTL analysis||[http://statgen.ncsu.edu/eQTLViewer/ eQTLViewer]||GPL||depends on perl||free||no||
||Association analysis||[http://pngu.mgh.harvard.edu/~purcell/plink PLINK]||GPL||Looks simple||free||no||
||Haplotype analysis||[http://www.broad.mit.edu/mpg/haploview Haploview]||MIT||depends on java||free||no||
||Analysis of recombination histories||[http://www.stats.ox.ac.uk/~lyngsoe/beagle/ Beagle]||LGPL||depends on C and python||free||no||
||Detection of microsatellites||[http://code.google.com/p/msatcommander/ Msatcommander]||GPL||Depense on wxpython, biopython, primer3||free||no||
||QTL analysis||[[http://statgen.ncsu.edu/eQTLViewer/|eQTLViewer]]||GPL||depends on perl||free||no||
||Association analysis||[[http://pngu.mgh.harvard.edu/~purcell/plink|PLINK]]||GPL||Looks simple||free||no||
||Haplotype analysis||[[http://www.broad.mit.edu/mpg/haploview|Haploview]]||MIT||depends on java||free||no||
||Analysis of recombination histories||[[http://www.stats.ox.ac.uk/~lyngsoe/beagle/|Beagle]]||LGPL||depends on C and python||free||no||
||Detection of microsatellites||[[http://code.google.com/p/msatcommander/|Msatcommander]]||GPL||Depense on wxpython, biopython, primer3||free||no||
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Back to ["DebianScience/Biology"] Back to [[DebianScience/Biology]]

Task

Name

Licence

Packaging

Importance

Listed on microbio.wml?

Hapoltyping

Hotspotter

no licence

did not build out of the box on ppc

no

Association studies

altree

as Perl itself

unofficial (ens-lyon)

free

no

Linkage desequilibrium studies

SUP

GPL

Depends on FastSLINK

free

no

QTL / SNP analysis

happy

free

R package

free

no

QTL analysis

R/qtl

free

Debian R package r-cran-qtl

important

?

QTL analysis

eQTLViewer

GPL

depends on perl

free

no

Association analysis

PLINK

GPL

Looks simple

free

no

Haplotype analysis

Haploview

MIT

depends on java

free

no

Analysis of recombination histories

Beagle

LGPL

depends on C and python

free

no

Detection of microsatellites

Msatcommander

GPL

Depense on wxpython, biopython, primer3

free

no

Linkage disequilibrium mapping

http://www.daimi.au.dk/~mailund/HapCluster/ ?HapCluster++

GPL

rpms available

free, up-to-date

no

Task

Name

Licence

Packaging

Importance

Listed on microbio.wml?


Back to DebianScience/Biology