This beat is now ready to have Fedora 25 content added by the beat writer
BEDtools
BEDTools is a set of utilities allow to one to address common genomics tasks such as finding feature overlaps and computing coverage. BEDtools is new to Fedora.
R
R is a popular statistics package with many add on packages to address specific needs. Fedora 15 brings a few new add-on packages to R.
R-GenomicRanges
R-GenomicRanges provides general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.
http://www.bioconductor.org/packages/release/bioc/html/GenomicRanges.html
R-ROC
The ROC library is a collection of R classes and functions related to receiver operating characteristic (ROC) curves. These functions are targeted at the use of ROC analysis with DNA microarrays The R-ROC package provides a set of utilities for ROC.
http://bioconductor.org/packages/release/bioc/html/ROC.html
R-affydata
R-affydata is a set of example affymetrix datasets. These datasets are somewhat larger than the examples included in the affy package, and are intended to better represent "real-world" datasets.
http://www.bioconductor.org/packages/2.6/data/experiment/html/affydata.html
NOTE: The following packages are new for F15, _might_ be included
R-GenomicRanges new 1.2.3 http://www.bioconductor.org/packages/release/bioc/html/GenomicRanges.html
R-ROC new 1.24.1 http://bioconductor.org/packages/release/bioc/html/ROC.html
R-affydata new 1.11.10 http://www.bioconductor.org/packages/2.6/data/experiment/html/affydata.html
ape new 1.1.0 http://www.tddft.org/programs/APE
coot new 0.6.2 http://www.biop.ox.ac.uk/coot/ coot-doc new 0.6.2 http://www.biop.ox.ac.uk/coot/
cp2k new 2.1 http://cp2k.berlios.de/ cp2k-common new 2.1 http://cp2k.berlios.de/ cp2k-smp new 2.1 http://cp2k.berlios.de/
dia-optics new 0.1 http://dia-installer.de/shapes/optics/index_en.html
flterm new 0.9 http://milkymist.org
gpsbabel-gui new 1.4.2 http://www.gpsbabel.org
gretl new 1.9.3 http://gretl.sourceforge.net/
libxc new 1.0 http://www.tddft.org/programs/octopus/wiki/index.php/Libxc
ltl2ba new 1.1 http://www.lsv.ens-cachan.fr/~gastin/ltl2ba/
mot-adms new 2.2.9 http://mot-adms.sourceforge.net/
mpich2-mpd new 1.3.2 http://www.mcs.anl.gov/research/projects/mpich2
nesc new 1.3.2 http://nescc.sourceforge.net/
openeuclide new 0.5 http://coulon.publi.free.fr/openeuclide/index.php
plotdrop new 0.5.3 http://plotdrop.sourceforge.net/
psfex new 3.9.1 http://astromatic.iap.fr/software/psfex
qd new 2.3.11 http://crd.lbl.gov/~dhbailey/mpdist/
root-genetic new 5.28.00 http://root.cern.ch/
root-graf-fitsio new 5.28.00 http://root.cern.ch/
root-hist-factory new 5.28.00 http://root.cern.ch/
root-io new 5.28.00 http://root.cern.ch/
root-proof-pq2 new 5.28.00 http://root.cern.ch/
votca-csg new 1.0.1 http://www.votca.org
votca-csg-common new 1.0.1 http://www.votca.org
votca-tools new 1.0.1 http://www.votca.org
why-all new 2.28 http://why.lri.fr/