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| === BEDtools ===
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| '''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.
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| === R ===
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| '''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.
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| ==== R-GenomicRanges ====
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| '''R-GenomicRanges''' provides general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.
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| http://www.bioconductor.org/packages/release/bioc/html/GenomicRanges.html
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| ==== R-ROC ====
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| The ROC library is a collection of R classes and functions related to receiver
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| operating characteristic (ROC) curves. These functions are targeted at the use
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| of ROC analysis with DNA microarrays The '''R-ROC''' package provides a set of utilities for ROC.
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| http://bioconductor.org/packages/release/bioc/html/ROC.html
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| ==== R-affydata ====
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| '''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.
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| http://www.bioconductor.org/packages/2.6/data/experiment/html/affydata.html
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| === APE ===
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| '''ape''' (Atomic Pseudopotential Engine) is a tool for generating atomic pseudopotentials within a Density-Functional Theory framework. It is distributed under the GPL and it produces pseudopotential files suitable for use with
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| * SIESTA
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| * OCTOPUS
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| * ABINIT
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| * PWscf
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| http://www.tddft.org/programs/APE/node/9
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| === coot ===
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| '''coot''' (Crystallographic Object-Oriented Toolkit) is a set of tools for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. '''coot''' 0.6.2 is included in Fedora 15.
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| http://www.biop.ox.ac.uk/coot/
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| === cp2k ===
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| '''cp2k''' is a program to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
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| Fedora 15 includes '''cp2k''' version 2.1. For details refer to http://cp2k.berlios.de/
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| === dia-optics ===
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| '''dia-optics''' is a shape library for the popular '''dia''' drawing package. The included shapes may be reviewed at http://dia-installer.de/shapes/optics/index_en.html
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| === gpsbabel-gui ===
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| '''gpsbabel''' is a package for manipulating GPS data from a variety of devices and manipulating that data. Fedora 15 now includes a GUI for that data. Refer to http://www.gpsbabel.org/ for additional information.
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| === gretl ===
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| '''gretl''' is a cross-platform software package for econometric analysis. It includes links to '''R''', '''octave''' and '''ox''' for more detailed analysis. A full list of features may be found at http://gretl.sourceforge.net/
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| '''NOTE: The following packages are new for F15, _might_ be included'''
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| libxc new 1.0 http://www.tddft.org/programs/octopus/wiki/index.php/Libxc
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| ltl2ba new 1.1 http://www.lsv.ens-cachan.fr/~gastin/ltl2ba/
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| mot-adms new 2.2.9 http://mot-adms.sourceforge.net/
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| mpich2-mpd new 1.3.2 http://www.mcs.anl.gov/research/projects/mpich2
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| nesc new 1.3.2 http://nescc.sourceforge.net/
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| openeuclide new 0.5 http://coulon.publi.free.fr/openeuclide/index.php
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| plotdrop new 0.5.3 http://plotdrop.sourceforge.net/
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| psfex new 3.9.1 http://astromatic.iap.fr/software/psfex
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| qd new 2.3.11 http://crd.lbl.gov/~dhbailey/mpdist/
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| root-genetic new 5.28.00 http://root.cern.ch/
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| root-graf-fitsio new 5.28.00 http://root.cern.ch/
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| root-hist-factory new 5.28.00 http://root.cern.ch/
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| root-io new 5.28.00 http://root.cern.ch/
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| root-proof-pq2 new 5.28.00 http://root.cern.ch/
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| votca-csg new 1.0.1 http://www.votca.org
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| votca-csg-common new 1.0.1 http://www.votca.org
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| votca-tools new 1.0.1 http://www.votca.org
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| why-all new 2.28 http://why.lri.fr/
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| | {{Docs_beat_closed}} |
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| [[Category:Docs Project]] | | [[Category:Docs Project]] |
| [[Category:Draft documentation]] | | [[Category:Draft documentation]] |
| [[Category:Documentation beats]] | | [[Category:Documentation beats]] |
