Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Browse files

Manifest configuration files for CloudBioLinux release 27 June 2012

  • Loading branch information...
commit 16a3560d5e7bda89da6ab8a379e9757f1c14535e 1 parent 4d25842
@chapmanb authored
View
296 manifest/custom-packages.yaml
@@ -0,0 +1,296 @@
+abyss:
+ description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence
+ assembler.
+ homepage_uri: http://www.bcgsc.ca/platform/bioinfo/software/abyss
+ name: abyss
+ version: 1.3.3
+beast:
+ description: 'BEAST: Bayesian MCMC analysis of molecular sequences.'
+ homepage_uri: http://beast.bio.ed.ac.uk/main_page
+ name: beast
+ version: ''
+bedtools:
+ description: A flexible suite of utilities for comparing genomic features.
+ homepage_uri: https://code.google.com/p/bedtools/
+ name: bedtools
+ version: github
+bfast:
+ description: 'BFAST: Blat-like Fast Accurate Search Tool.'
+ homepage_uri: http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page
+ name: bfast
+ version: 0.7.0
+bio4j:
+ description: Bio4j graph based database built on Neo4j with UniProt, GO, RefSeq
+ and more.
+ homepage_uri: http://www.bio4j.com/
+ name: bio4j
+ version: '0.7'
+bowtie:
+ description: The bowtie short read aligner.
+ homepage_uri: http://bowtie-bio.sourceforge.net/index.shtml
+ name: bowtie
+ version: 0.12.7
+bowtie2:
+ description: bowtie2 short read aligner, with gap support.
+ homepage_uri: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
+ name: bowtie2
+ version: 2.0.0-beta6
+bwa:
+ description: 'BWA: aligns short nucleotide sequences against a long reference sequence.'
+ homepage_uri: http://bio-bwa.sourceforge.net/
+ name: bwa
+ version: 0.5.9
+bx_python:
+ description: Tools for manipulating biological data, particularly multiple sequence
+ alignments
+ homepage_uri: https://bitbucket.org/james_taylor/bx-python/wiki/Home
+ name: bx_python
+ version: bitbucket
+cljr:
+ description: Clojure package manager, cljr.
+ homepage_uri: http://github.com/liebke/cljr
+ name: cljr
+ version: ''
+cloudman:
+ description: ' A meta method for installing all of CloudMan components.'
+ homepage_uri: ''
+ name: cloudman
+ version: ''
+crisp:
+ description: Detect SNPs and short indels from pooled sequencing data.
+ homepage_uri: https://sites.google.com/site/vibansal/software/crisp/
+ name: crisp
+ version: '5'
+cufflinks:
+ description: Cufflinks assembles transcripts, estimates their abundances, and tests
+ for differential expression and regulation in RNA-Seq samples.
+ homepage_uri: http://cufflinks.cbcb.umd.edu/
+ name: cufflinks
+ version: 2.0.0
+dwgsim:
+ description: 'DWGSIM: simulating NGS data and evaluating mappings and variant calling.'
+ homepage_uri: http://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Main_Page
+ name: dwgsim
+ version: 0.1.8
+echo:
+ description: 'ECHO: A reference-free short-read error correction algorithm'
+ homepage_uri: http://uc-echo.sourceforge.net/
+ name: echo
+ version: '1_11'
+emboss:
+ description: 'EMBOSS: A high-quality package of free, Open Source software for molecular
+ biology.'
+ homepage_uri: http://emboss.sourceforge.net/
+ name: emboss
+ version: 6.3.1
+fastqc:
+ description: A quality control tool for high throughput sequence data.
+ homepage_uri: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+ name: fastqc
+ version: 0.10.1
+fastx_toolkit:
+ description: 'FASTX-Toolkit: collection of command line tools for Short-Reads FASTA/FASTQ
+ files preprocessing.'
+ homepage_uri: http://hannonlab.cshl.edu/fastx_toolkit/
+ name: fastx_toolkit
+ version: 0.0.13
+freebayes:
+ description: Bayesian haplotype-based polymorphism discovery and genotyping.
+ homepage_uri: https://github.com/ekg/freebayes
+ name: freebayes
+ version: github
+gatk:
+ description: 'GATK: library for writing efficient analysis tools using next-generation
+ sequencing data '
+ homepage_uri: http://www.broadinstitute.org/gsa/wiki/index.php/Home_Page
+ name: gatk
+ version: 1.6-11-g3b2fab9
+gatk_queue:
+ description: Command-line scripting framework for defining multi-stage genomic analysis
+ pipelines.
+ homepage_uri: http://www.broadinstitute.org/gsa/wiki/index.php/GATK-Queue
+ name: gatk_queue
+ version: 1.6-11-g3b2fab9
+gmap:
+ description: 'GMAP and GSNAP: A Genomic Mapping and Alignment Program for mRNA EST
+ and short reads.'
+ homepage_uri: http://research-pub.gene.com/gmap/
+ name: gmap
+ version: '2011-11-12'
+hydra:
+ description: Hydra detects structural variation breakpoints in both unique and duplicated
+ genomic regions.
+ homepage_uri: https://code.google.com/p/hydra-sv/
+ name: hydra
+ version: 0.5.3
+lastz:
+ description: LASTZ sequence alignment program.
+ homepage_uri: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html
+ name: lastz
+ version: 1.02.00
+leinengin:
+ description: Clojure tool for project configuration and automation.
+ homepage_uri: http://github.com/technomancy/leiningen
+ name: leinengin
+ version: ''
+macs:
+ description: Model-based Analysis for ChIP-Seq.
+ homepage_uri: http://liulab.dfci.harvard.edu/MACS/
+ name: macs
+ version: 1.4.2
+matplotlib:
+ description: matplotlib is a python 2D plotting library which produces publication
+ quality figures
+ homepage_uri: http://matplotlib.sourceforge.net/
+ name: matplotlib
+ version: 1.0.1
+mosaik:
+ description: 'MOSAIK: reference-guided aligner for next-generation sequencing technologies'
+ homepage_uri: http://code.google.com/p/mosaik-aligner/
+ name: mosaik
+ version: github
+nginx:
+ description: Nginx open source web server.
+ homepage_uri: http://www.nginx.org/
+ name: nginx
+ version: 1.2.0
+novoalign:
+ description: Novoalign short read aligner using Needleman-Wunsch algorithm with
+ affine gap penalties.
+ homepage_uri: http://www.novocraft.com/main/index.php
+ name: novoalign
+ version: V2.08.01
+perm:
+ description: Efficient mapping of short sequences accomplished with periodic full
+ sensitive spaced seeds.
+ homepage_uri: https://code.google.com/p/perm/
+ name: perm
+ version: '3.6'
+pgdspider:
+ description: PGDSpider format conversion for population genetics programs.
+ homepage_uri: http://www.cmpg.unibe.ch/software/PGDSpider/
+ name: pgdspider
+ version: 2.0.1.2
+picard:
+ description: Command-line utilities that manipulate BAM files with a Java API.
+ homepage_uri: http://picard.sourceforge.net/
+ name: picard
+ version: '1.68'
+plink_seq:
+ description: A toolset for working with human genetic variation data.
+ homepage_uri: http://atgu.mgh.harvard.edu/plinkseq/
+ name: plink_seq
+ version: '0.08'
+proftpd:
+ description: Highly configurable GPL-licensed FTP server software.
+ homepage_uri: http://proftpd.org/
+ name: proftpd
+ version: 1.3.4a
+pydoop:
+ description: pydoop; provides Hadoop access for Python.
+ homepage_uri: http://pydoop.sourceforge.net/docs/
+ name: pydoop
+ version: ''
+rpy:
+ description: RPy is a very simple, yet robust, Python interface to the R Programming
+ Language.
+ homepage_uri: http://rpy.sourceforge.net/
+ name: rpy
+ version: 1.0.3
+s3fs:
+ description: FUSE-based file system backed by Amazon S3.
+ homepage_uri: https://code.google.com/p/s3fs/
+ name: s3fs
+ version: '1.61'
+samtools:
+ description: SAM Tools provide various utilities for manipulating alignments in
+ the SAM format.
+ homepage_uri: http://samtools.sourceforge.net/
+ name: samtools
+ version: 0.1.18
+seal:
+ description: 'Install seal: process high-throughput sequencing with Hadoop.'
+ homepage_uri: http://biodoop-seal.sf.net/
+ name: seal
+ version: ''
+sge:
+ description: Sun Grid Engine.
+ homepage_uri: ''
+ name: sge
+ version: ''
+shrec:
+ description: Shrec is a bioinformatics tool for error correction of HTS read data.
+ homepage_uri: http://sourceforge.net/projects/shrec-ec/
+ name: shrec
+ version: '2.2'
+snpeff:
+ description: Variant annotation and effect prediction tool.
+ homepage_uri: http://snpeff.sourceforge.net/
+ name: snpeff
+ version: '2_0_5'
+solexaqa:
+ description: SolexaQA creates visual representations of data quality from FASTQ
+ files.
+ homepage_uri: http://solexaqa.sourceforge.net/
+ name: solexaqa
+ version: '1.4'
+stacks:
+ description: 'Stacks: build loci out of a set of short-read sequenced samples.'
+ homepage_uri: http://creskolab.uoregon.edu/stacks/
+ name: stacks
+ version: '0.998'
+stampy:
+ description: 'Stampy: mapping of short reads from illumina sequencing machines onto
+ a reference genome.'
+ homepage_uri: http://www.well.ox.ac.uk/project-stampy
+ name: stampy
+ version: 1.0.15
+tassel:
+ description: 'TASSEL: evaluate traits associations, evolutionary patterns, and linkage
+ disequilibrium.'
+ homepage_uri: http://www.maizegenetics.net/index.php?option=com_content&task=view&id=89&Itemid=119
+ name: tassel
+ version: '3.0'
+tophat:
+ description: TopHat is a fast splice junction mapper for RNA-Seq reads
+ homepage_uri: http://tophat.cbcb.umd.edu/
+ name: tophat
+ version: 2.0.0
+tracer:
+ description: A program for analysing results from Bayesian MCMC programs such as
+ BEAST & MrBayes.
+ homepage_uri: http://beast.bio.ed.ac.uk/main_page
+ name: tracer
+ version: ''
+transabyss:
+ description: Analyze ABySS multi-k-assembled shotgun transcriptome data.
+ homepage_uri: http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
+ name: transabyss
+ version: 1.3.2
+trinity:
+ description: Efficient and robust de novo reconstruction of transcriptomes from
+ RNA-seq data.
+ homepage_uri: http://trinityrnaseq.sourceforge.net/
+ name: trinity
+ version: r2012-05-18
+ucsc_tools:
+ description: Useful executables from UCSC.
+ homepage_uri: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
+ name: ucsc_tools
+ version: ''
+varianttools:
+ description: Annotation, selection, and analysis of variants in the context of next-gen
+ sequencing analysis.
+ homepage_uri: http://varianttools.sourceforge.net/
+ name: varianttools
+ version: 1.0.1
+vcftools:
+ description: Work with VCF files, such as those generated by the 1000 Genomes Project.
+ homepage_uri: http://vcftools.sourceforge.net/
+ name: vcftools
+ version: 0.1.7
+velvet:
+ description: Sequence assembler for very short reads.
+ homepage_uri: http://www.ebi.ac.uk/~zerbino/velvet/
+ name: velvet
+ version: 1.2.05
View
18,911 manifest/debian-packages.yaml
18,911 additions, 0 deletions not shown
View
846 manifest/python-packages.yaml
@@ -0,0 +1,846 @@
+BeautifulSoup:
+ description: HTML/XML parser for quick-turnaround applications like screen-scraping.
+ homepage_uri: http://www.crummy.com/software/BeautifulSoup/
+ name: BeautifulSoup
+ version: 3.2.1
+Brlapi:
+ description: Python BrlAPI
+ homepage_uri: http://mielke.cc/brltty/
+ name: Brlapi
+ version: 0.5.6
+Cheetah:
+ description: Cheetah is a template engine and code generation tool.
+ homepage_uri: http://www.cheetahtemplate.org/
+ name: Cheetah
+ version: 2.4.4
+CouchDB:
+ description: Python library for working with CouchDB
+ homepage_uri: http://code.google.com/p/couchdb-python/
+ name: CouchDB
+ version: '0.8'
+Cython:
+ description: The Cython compiler for writing C extensions for the Python language.
+ homepage_uri: http://www.cython.org
+ name: Cython
+ version: '0.16'
+DendroPy:
+ description: 'A Python library for phylogenetics and phylogenetic computing: reading,
+ writing, simulation, processing and manipulation of phylogenetic trees (phylogenies)
+ and characters.'
+ homepage_uri: http://packages.python.org/DendroPy/
+ name: DendroPy
+ version: 3.11.0
+Fabric:
+ description: Fabric is a simple, Pythonic tool for remote execution and deployment.
+ homepage_uri: http://fabfile.org
+ name: Fabric
+ version: 1.4.2
+GnuPGInterface:
+ description: GnuPG interactions with file handles
+ homepage_uri: http://py-gnupg.sourceforge.net/
+ name: GnuPGInterface
+ version: 0.3.2
+HTSeq:
+ description: A framework to process and analyze data from high-throughput sequencing
+ (HTS) assays
+ homepage_uri: http://www-huber.embl.de/users/anders/HTSeq/
+ name: HTSeq
+ version: 0.5.3p7
+Jinja2:
+ description: A small but fast and easy to use stand-alone template engine written
+ in pure python.
+ homepage_uri: http://jinja.pocoo.org/
+ name: Jinja2
+ version: '2.6'
+Landscape Client:
+ description: Landscape Client
+ homepage_uri: http://landscape.canonical.com
+ name: Landscape Client
+ version: 12.04.2
+Logbook:
+ description: A logging replacement for Python
+ homepage_uri: http://logbook.pocoo.org/
+ name: Logbook
+ version: '0.3'
+M2Crypto:
+ description: 'M2Crypto: A Python crypto and SSL toolkit'
+ homepage_uri: http://chandlerproject.org/Projects/MeTooCrypto
+ name: M2Crypto
+ version: 0.21.1
+MACS:
+ description: Model Based Analysis for ChIP-Seq data
+ homepage_uri: http://liulab.dfci.harvard.edu/MACS/
+ name: MACS
+ version: 1.4.2
+Magic file extensions:
+ description: libmagic Python bindings
+ homepage_uri: UNKNOWN
+ name: Magic file extensions
+ version: '0.2'
+Mako:
+ description: A super-fast templating language that borrows the best ideas from
+ the existing templating languages.
+ homepage_uri: http://www.makotemplates.org/
+ name: Mako
+ version: 0.7.0
+MarkupSafe:
+ description: Implements a XML/HTML/XHTML Markup safe string for Python
+ homepage_uri: http://dev.pocoo.org/
+ name: MarkupSafe
+ version: '0.15'
+MySQL-python:
+ description: Python interface to MySQL
+ homepage_uri: http://sourceforge.net/projects/mysql-python
+ name: MySQL-python
+ version: 1.2.3
+PAM:
+ description: Python bindings for PAM
+ homepage_uri: UNKNOWN
+ name: PAM
+ version: 0.4.2
+PIL:
+ description: Python Imaging Library
+ homepage_uri: http://www.pythonware.com/products/pil
+ name: PIL
+ version: 1.1.7
+Paste:
+ description: Tools for using a Web Server Gateway Interface stack
+ homepage_uri: http://pythonpaste.org
+ name: Paste
+ version: 1.7.5.1
+PasteDeploy:
+ description: Load, configure, and compose WSGI applications and servers
+ homepage_uri: http://pythonpaste.org/deploy/
+ name: PasteDeploy
+ version: 1.5.0
+PasteScript:
+ description: A pluggable command-line frontend, including commands to setup package
+ file layouts
+ homepage_uri: http://pythonpaste.org/script/
+ name: PasteScript
+ version: 1.7.5
+PyVCF:
+ description: Variant Call Format (VCF) parser for Python
+ homepage_uri: https://github.com/jamescasbon/PyVCF
+ name: PyVCF
+ version: 0.4.6
+PyYAML:
+ description: YAML parser and emitter for Python
+ homepage_uri: http://pyyaml.org/wiki/PyYAML
+ name: PyYAML
+ version: '3.10'
+Pygments:
+ description: Pygments is a syntax highlighting package written in Python.
+ homepage_uri: http://pygments.org/
+ name: Pygments
+ version: '1.5'
+Pyrex:
+ description: UNKNOWN
+ homepage_uri: http://www.cosc.canterbury.ac.nz/~greg/python/Pyrex/
+ name: Pyrex
+ version: 0.9.9
+Pyste:
+ description: Pyste - Python Semi-Automatic Exporter
+ homepage_uri: http://www.boost.org/libs/python/pyste/index.html
+ name: Pyste
+ version: 0.9.10
+Python:
+ description: A high-level object-oriented programming language
+ homepage_uri: http://www.python.org/2.7
+ name: Python
+ version: 2.7.3
+Routes:
+ description: Routing Recognition and Generation Tools
+ homepage_uri: http://routes.groovie.org/
+ name: Routes
+ version: 1.12.3
+SQLAlchemy:
+ description: Database Abstraction Library
+ homepage_uri: http://www.sqlalchemy.org
+ name: SQLAlchemy
+ version: 0.7.8
+Sphinx:
+ description: Python documentation generator
+ homepage_uri: http://sphinx.pocoo.org/
+ name: Sphinx
+ version: 1.1.3
+StarCluster:
+ description: StarCluster is a utility for creating and managing computing clusters
+ hosted on Amazon's Elastic Compute Cloud (EC2).
+ homepage_uri: http://web.mit.edu/starcluster
+ name: StarCluster
+ version: 0.93.3
+Twisted:
+ description: An asynchronous networking framework written in Python
+ homepage_uri: http://twistedmatrix.com/
+ name: Twisted
+ version: 12.1.0
+Twisted Core:
+ description: The core parts of the Twisted networking framework
+ homepage_uri: http://twistedmatrix.com/
+ name: Twisted Core
+ version: 11.1.0
+Twisted Names:
+ description: A Twisted DNS implementation.
+ homepage_uri: http://twistedmatrix.com/trac/wiki/TwistedNames
+ name: Twisted Names
+ version: 11.1.0
+Twisted Web:
+ description: Twisted web server, programmable in Python.
+ homepage_uri: http://twistedmatrix.com/trac/wiki/TwistedWeb
+ name: Twisted Web
+ version: 11.1.0
+VTK:
+ description: The Visualization Toolkit
+ homepage_uri: http://www.vtk.org/
+ name: VTK
+ version: 5.8.0
+WebHelpers:
+ description: Web Helpers
+ homepage_uri: http://webhelpers.groovie.org/
+ name: WebHelpers
+ version: '1.3'
+WebOb:
+ description: WSGI request and response object
+ homepage_uri: http://webob.org/
+ name: WebOb
+ version: 1.2b2
+adium-theme-ubuntu:
+ description: UNKNOWN
+ homepage_uri: UNKNOWN
+ name: adium-theme-ubuntu
+ version: 0.3.2
+amqplib:
+ description: AMQP Client Library
+ homepage_uri: http://code.google.com/p/py-amqplib/
+ name: amqplib
+ version: 1.0.2
+anyjson:
+ description: Wraps the best available JSON implementation available in a common
+ interface
+ homepage_uri: http://bitbucket.org/runeh/anyjson
+ name: anyjson
+ version: 0.3.1
+apptools:
+ description: application tools
+ homepage_uri: http://code.enthought.com/projects/app_tools.php
+ name: apptools
+ version: 4.0.0
+apt-xapian-index:
+ description: Xapian index of Debian packages
+ homepage_uri: http://www.enricozini.org/sw/apt-xapian-index/
+ name: apt-xapian-index
+ version: '0.44'
+apturl:
+ description: UNKNOWN
+ homepage_uri: UNKNOWN
+ name: apturl
+ version: 0.5.1ubuntu3
+argparse:
+ description: Python command-line parsing library
+ homepage_uri: ''
+ name: argparse
+ version: 1.2.1
+bcbio-nextgen:
+ description: Automated, distributed next-gen sequencing pipeline; includes Galaxy
+ interaction
+ homepage_uri: https://github.com/chapmanb/bcbb/tree/master/nextgen
+ name: bcbio-nextgen
+ version: '0.2'
+biopython:
+ description: Freely available tools for computational molecular biology.
+ homepage_uri: http://www.biopython.org/
+ name: biopython
+ version: '1.59'
+boto:
+ description: Amazon Web Services Library
+ homepage_uri: https://github.com/boto/boto/
+ name: boto
+ version: 2.5.1
+bx-python:
+ description: Tools for manipulating biological data, particularly multiple sequence
+ alignments
+ homepage_uri: http://bitbucket.org/james_taylor/bx-python/wiki/Home
+ name: bx-python
+ version: 0.7.1
+bzr:
+ description: Friendly distributed version control system
+ homepage_uri: http://bazaar.canonical.com/
+ name: bzr
+ version: 2.5.0
+celery:
+ description: Distributed Task Queue
+ homepage_uri: http://celeryproject.org
+ name: celery
+ version: 2.5.5
+chardet:
+ description: Universal encoding detector
+ homepage_uri: http://chardet.feedparser.org/
+ name: chardet
+ version: 2.0.1
+cloud-init:
+ description: EC2 initialisation magic
+ homepage_uri: http://launchpad.net/cloud-init/
+ name: cloud-init
+ version: 0.6.3
+command-not-found:
+ description: UNKNOWN
+ homepage_uri: UNKNOWN
+ name: command-not-found
+ version: 0.2.44
+configglue:
+ description: Glue to stick OptionParser and ConfigParser together
+ homepage_uri: https://launchpad.net/configglue
+ name: configglue
+ version: '1.0'
+configobj:
+ description: Config file reading, writing and validation.
+ homepage_uri: http://www.voidspace.org.uk/python/configobj.html
+ name: configobj
+ version: 4.7.2
+debtagshw:
+ description: UNKNOWN
+ homepage_uri: UNKNOWN
+ name: debtagshw
+ version: '0.1'
+decorator:
+ description: Better living through Python with decorators
+ homepage_uri: http://pypi.python.org/pypi/decorator
+ name: decorator
+ version: 3.3.1
+defer:
+ description: Simple framework for asynchronous programming
+ homepage_uri: http://launchpad.net/python-defer
+ name: defer
+ version: 1.0.2
+devscripts:
+ description: UNKNOWN
+ homepage_uri: UNKNOWN
+ name: devscripts
+ version: 2.11.6ubuntu1.2
+dirspec:
+ description: XDG Base and User directories implementation
+ homepage_uri: https://launchpad.net/dirspec
+ name: dirspec
+ version: 3.0.0
+distribute:
+ description: Easily download, build, install, upgrade, and uninstall Python packages
+ homepage_uri: http://packages.python.org/distribute
+ name: distribute
+ version: 0.6.19
+docutils:
+ description: Docutils -- Python Documentation Utilities
+ homepage_uri: http://docutils.sourceforge.net/
+ name: docutils
+ version: 0.9.1
+duplicity:
+ description: Encrypted backup using rsync algorithm
+ homepage_uri: http://duplicity.nongnu.org/index.html
+ name: duplicity
+ version: 0.6.18
+envisage:
+ description: extensible application framework
+ homepage_uri: http://code.enthought.com/projects/envisage/
+ name: envisage
+ version: 4.0.0
+euca2ools:
+ description: Elastic Utility Computing Architecture Command Line Tools
+ homepage_uri: http://open.eucalyptus.com
+ name: euca2ools
+ version: 2.0.0
+gnuplot-py:
+ description: A Python interface to the gnuplot plotting program.
+ homepage_uri: http://gnuplot-py.sourceforge.net
+ name: gnuplot-py
+ version: '1.8'
+h5py:
+ description: Read and write HDF5 files from Python
+ homepage_uri: http://h5py.alfven.org
+ name: h5py
+ version: 2.0.1
+httplib2:
+ description: A comprehensive HTTP client library.
+ homepage_uri: http://code.google.com/p/httplib2/
+ name: httplib2
+ version: 0.7.2
+ipython:
+ description: 'IPython: Productive Interactive Computing'
+ homepage_uri: http://ipython.org
+ name: ipython
+ version: 0.12.1
+jockey:
+ description: UI for managing third-party and non-free drivers
+ homepage_uri: https://launchpad.net/jockey
+ name: jockey
+ version: 0.9.7
+keyring:
+ description: Store and access your passwords safely.
+ homepage_uri: http://bitbucket.org/kang/python-keyring-lib
+ name: keyring
+ version: 0.7.1
+kombu:
+ description: Messaging Framework for Python
+ homepage_uri: http://github.com/ask/kombu/
+ name: kombu
+ version: 2.1.8
+language-selector:
+ description: UNKNOWN
+ homepage_uri: UNKNOWN
+ name: language-selector
+ version: '0.1'
+launchpadlib:
+ description: Script Launchpad through its web services interfaces. Officially supported.
+ homepage_uri: https://help.launchpad.net/API/launchpadlib
+ name: launchpadlib
+ version: 1.9.12
+lazr.restfulclient:
+ description: A programmable client library that takes advantage of the commonalities
+ among
+ homepage_uri: https://launchpad.net/lazr.restfulclient
+ name: lazr.restfulclient
+ version: 0.12.0
+lazr.uri:
+ description: A self-contained, easily reusable library for parsing, manipulating,
+ homepage_uri: https://launchpad.net/lazr.uri
+ name: lazr.uri
+ version: 1.0.3
+louis:
+ description: Python bindings for liblouis
+ homepage_uri: ''
+ name: louis
+ version: 2.3.0
+lxml:
+ description: Powerful and Pythonic XML processing library combining libxml2/libxslt
+ with the ElementTree API.
+ homepage_uri: http://lxml.de/
+ name: lxml
+ version: 2.3.4
+matplotlib:
+ description: Python plotting package
+ homepage_uri: http://matplotlib.sourceforge.net
+ name: matplotlib
+ version: 1.0.1
+mayavi:
+ description: The Mayavi scientific data 3-dimensional visualizer.
+ homepage_uri: http://code.enthought.com/projects/mayavi/
+ name: mayavi
+ version: 4.0.0
+mercurial:
+ description: Scalable distributed SCM
+ homepage_uri: http://mercurial.selenic.com/
+ name: mercurial
+ version: 2.0.2
+networkx:
+ description: Python package for creating and manipulating graphs and networks
+ homepage_uri: http://networkx.lanl.gov/
+ name: networkx
+ version: 1.7rc1
+nose:
+ description: nose extends unittest to make testing easier
+ homepage_uri: http://readthedocs.org/docs/nose/
+ name: nose
+ version: 1.1.2
+numpy:
+ description: 'NumPy: array processing for numbers, strings, records, and objects.'
+ homepage_uri: http://numpy.scipy.org
+ name: numpy
+ version: 1.6.2
+nvidia-common:
+ description: Find obsolete NVIDIA drivers
+ homepage_uri: http://www.albertomilone.com
+ name: nvidia-common
+ version: 0.0.0
+oauth:
+ description: Library for OAuth version 1.0a.
+ homepage_uri: http://code.google.com/p/oauth
+ name: oauth
+ version: 1.0.1
+oca:
+ description: Bindings for XMLRPC OpenNebula Cloud API
+ homepage_uri: https://github.com/lukaszo/python-oca
+ name: oca
+ version: 0.2.3
+onboard:
+ description: Simple On-screen Keyboard
+ homepage_uri: http://launchpad.net/onboard/
+ name: onboard
+ version: 0.97.1
+oneconf:
+ description: UNKNOWN
+ homepage_uri: UNKNOWN
+ name: oneconf
+ version: 0.2.8.1
+pandas:
+ description: Powerful data structures for data analysis and statistics
+ homepage_uri: http://pandas.pydata.org
+ name: pandas
+ version: 0.7.3
+paramiko:
+ description: SSH2 protocol library
+ homepage_uri: http://www.lag.net/paramiko/
+ name: paramiko
+ version: 1.7.7.1
+pexpect:
+ description: Pexpect is a pure Python Expect. It allows easy control of other applications.
+ homepage_uri: http://pexpect.sourceforge.net/
+ name: pexpect
+ version: '2.3'
+pip:
+ description: pip installs packages. Python packages. An easy_install replacement
+ homepage_uri: http://www.pip-installer.org
+ name: pip
+ version: '1.1'
+piston-mini-client:
+ description: A package to consume Django-Piston web services
+ homepage_uri: https://launchpad.net/piston-mini-client
+ name: piston-mini-client
+ version: 0.7.2
+protobuf:
+ description: Protocol Buffers
+ homepage_uri: http://code.google.com/p/protobuf/
+ name: protobuf
+ version: 2.4.1
+psycopg2:
+ description: Python-PostgreSQL Database Adapter
+ homepage_uri: http://initd.org/psycopg/
+ name: psycopg2
+ version: 2.4.5
+pyOpenSSL:
+ description: Python wrapper module around the OpenSSL library
+ homepage_uri: http://pyopenssl.sourceforge.net/
+ name: pyOpenSSL
+ version: '0.13'
+pyasn1:
+ description: ASN.1 types and codecs
+ homepage_uri: http://sourceforge.net/projects/pyasn1/
+ name: pyasn1
+ version: 0.0.13b
+pybedtools:
+ description: Wrapper around BEDTools for bioinformatics work
+ homepage_uri: none
+ name: pybedtools
+ version: 0.6.1
+pycrypto:
+ description: Cryptographic modules for Python.
+ homepage_uri: http://www.pycrypto.org/
+ name: pycrypto
+ version: '2.6'
+pycups:
+ description: Python bindings for libcups
+ homepage_uri: http://cyberelk.net/tim/software/pycups/
+ name: pycups
+ version: 1.9.61
+pycurl:
+ description: PycURL -- cURL library module for Python
+ homepage_uri: http://pycurl.sourceforge.net/
+ name: pycurl
+ version: 7.19.0
+pydoop:
+ description: 'Pydoop: a Python MapReduce and HDFS API for Hadoop'
+ homepage_uri: http://pydoop.sourceforge.net
+ name: pydoop
+ version: 0.6.0
+pydot:
+ description: Python interface to Graphviz's Dot
+ homepage_uri: http://code.google.com/p/pydot/
+ name: pydot
+ version: 1.0.28
+pyface:
+ description: traits-capable windowing framework
+ homepage_uri: http://code.enthought.com/projects/traits_gui
+ name: pyface
+ version: 4.0.0
+pygooglechart:
+ description: A complete Python wrapper for the Google Chart API
+ homepage_uri: http://pygooglechart.slowchop.com/
+ name: pygooglechart
+ version: 0.3.0
+pygr:
+ description: Pygr, a Python graph-database toolkit oriented primarily on bioinformatics
+ homepage_uri: http://code.google.com/p/pygr/
+ name: pygr
+ version: 0.8.2
+pyinotify:
+ description: Linux filesystem events monitoring
+ homepage_uri: http://github.com/seb-m/pyinotify
+ name: pyinotify
+ version: 0.9.2
+pymongo:
+ description: Python driver for MongoDB <http://www.mongodb.org>
+ homepage_uri: http://github.com/mongodb/mongo-python-driver
+ name: pymongo
+ version: '2.2'
+pyparsing:
+ description: Python parsing module
+ homepage_uri: http://pyparsing.wikispaces.com/
+ name: pyparsing
+ version: 1.5.6
+pysam:
+ description: pysam
+ homepage_uri: http://code.google.com/p/pysam/
+ name: pysam
+ version: '0.6'
+pyserial:
+ description: Python Serial Port Extension
+ homepage_uri: http://pyserial.sourceforge.net/
+ name: pyserial
+ version: '2.5'
+pysmbc:
+ description: Python bindings for libsmbclient
+ homepage_uri: http://cyberelk.net/tim/software/pysmbc/
+ name: pysmbc
+ version: 1.0.13
+pysqlite:
+ description: DB-API 2.0 interface for SQLite 3.x
+ homepage_uri: http://pysqlite.googlecode.com/
+ name: pysqlite
+ version: 2.6.3
+python-apt:
+ description: Python bindings for APT
+ homepage_uri: UNKNOWN
+ name: python-apt
+ version: 0.8.3ubuntu7
+python-cjson:
+ description: Fast JSON encoder/decoder for Python
+ homepage_uri: http://ag-projects.com/
+ name: python-cjson
+ version: 1.0.5
+python-dateutil:
+ description: Extensions to the standard python 2.3+ datetime module
+ homepage_uri: http://labix.org/python-dateutil
+ name: python-dateutil
+ version: '1.5'
+python-debian:
+ description: Debian package related modules
+ homepage_uri: http://packages.debian.org/sid/python-debian
+ name: python-debian
+ version: 0.1.21ubuntu1
+python-distutils-extra:
+ description: Add support for i18n, documentation and icons to distutils
+ homepage_uri: UNKNOWN
+ name: python-distutils-extra
+ version: '2.32'
+python-virtkey:
+ description: python extension for emulating keypresses and getting keyboard layout
+ homepage_uri: https://launchpad.net/python-virtkey/
+ name: python-virtkey
+ version: 0.60.0
+pyxdg:
+ description: PyXDG contains implementations of freedesktop.org standards in python.
+ homepage_uri: http://cvs.freedesktop.org/cgi-bin/viewcvs.cgi/pyxdg/
+ name: pyxdg
+ version: '0.19'
+pyzmq:
+ description: Python bindings for 0MQ.
+ homepage_uri: http://github.com/zeromq/pyzmq
+ name: pyzmq
+ version: 2.2.0
+reportlab:
+ description: The Reportlab Toolkit
+ homepage_uri: http://www.reportlab.com/
+ name: reportlab
+ version: '2.5'
+repoze.lru:
+ description: A tiny LRU cache implementation and decorator
+ homepage_uri: http://www.repoze.org
+ name: repoze.lru
+ version: '0.5'
+rhythmbox-ubuntuone:
+ description: Ubuntu One Rhythmbox plug-in
+ homepage_uri: https://launchpad.net/rhythmbox-ubuntuone
+ name: rhythmbox-ubuntuone
+ version: 3.0.0
+rpy:
+ description: Python interface to the R language
+ homepage_uri: http://rpy.sourceforge.net
+ name: rpy
+ version: 1.0.3
+rpy2:
+ description: ''
+ homepage_uri: ''
+ name: rpy2
+ version: 2.2.6dev-20120618
+rpy2-bioconductor-extensions:
+ description: Bioconductor-specific extensions for rpy2
+ homepage_uri: no url yet
+ name: rpy2-bioconductor-extensions
+ version: 0.2.5-dev
+ruffus:
+ description: Light-weight Python Computational Pipeline Management
+ homepage_uri: http://ruffus.googlecode.com
+ name: ruffus
+ version: '2.2'
+scikits.learn:
+ description: A set of python modules for machine learning and data mining
+ homepage_uri: http://scikit-learn.sourceforge.net
+ name: scikits.learn
+ version: 0.8.1
+scikits.statsmodels:
+ description: Statistical computations and models for use with SciPy
+ homepage_uri: http://statsmodels.sourceforge.net/
+ name: scikits.statsmodels
+ version: 0.3.1
+scipy:
+ description: 'SciPy: Scientific Library for Python'
+ homepage_uri: http://www.scipy.org
+ name: scipy
+ version: 0.10.1
+seal:
+ description: 'Seal: Sequence Alignment on Hadoop.'
+ homepage_uri: http://www.crs4.it
+ name: seal
+ version: devel-20120618
+sessioninstaller:
+ description: APT based installer using PackageKit session DBus API
+ homepage_uri: UNKNOWN
+ name: sessioninstaller
+ version: 0.0.0
+setuptools:
+ description: xxxx
+ homepage_uri: xxx
+ name: setuptools
+ version: 0.6c11
+simplejson:
+ description: Simple, fast, extensible JSON encoder/decoder for Python
+ homepage_uri: http://github.com/simplejson/simplejson
+ name: simplejson
+ version: 2.5.2
+software-center-aptd-plugins:
+ description: UNKNOWN
+ homepage_uri: UNKNOWN
+ name: software-center-aptd-plugins
+ version: 0.0.0
+ssh:
+ description: SSH2 protocol library
+ homepage_uri: UNKNOWN
+ name: ssh
+ version: 1.7.14
+system-service:
+ description: UNKNOWN
+ homepage_uri: UNKNOWN
+ name: system-service
+ version: 0.1.6
+tornado:
+ description: Tornado is an open source version of the scalable, non-blocking web
+ server and and tools that power FriendFeed
+ homepage_uri: http://www.tornadoweb.org/
+ name: tornado
+ version: '2.3'
+traits:
+ description: explicitly typed attributes for Python
+ homepage_uri: http://code.enthought.com/projects/traits
+ name: traits
+ version: 4.0.0
+traitsui:
+ description: 'traitsui: traits-capable user interfaces'
+ homepage_uri: https://github.com/enthought/traitsui
+ name: traitsui
+ version: 4.0.1
+ubuntuone-couch:
+ description: Ubuntu One CouchDB
+ homepage_uri: https://launchpad.net/ubuntuone-couch
+ name: ubuntuone-couch
+ version: 0.3.0
+ubuntuone-installer:
+ description: Ubuntu One Installer
+ homepage_uri: https://launchpad.net/ubuntuone-installer
+ name: ubuntuone-installer
+ version: 3.0.0
+ubuntuone-storage-protocol:
+ description: UNKNOWN
+ homepage_uri: UNKNOWN
+ name: ubuntuone-storage-protocol
+ version: 3.0.0
+ufw:
+ description: front-end for Linux firewalling
+ homepage_uri: https://launchpad.net/ufw
+ name: ufw
+ version: 0.31.1-1
+unattended-upgrades:
+ description: UNKNOWN
+ homepage_uri: UNKNOWN
+ name: unattended-upgrades
+ version: '0.1'
+unity-lens-video:
+ description: UNKNOWN
+ homepage_uri: http://launchpad.net/~davidc3
+ name: unity-lens-video
+ version: 0.3.5
+unity-scope-video-remote:
+ description: UNKNOWN
+ homepage_uri: http://launchpad.net/onehundredscopes
+ name: unity-scope-video-remote
+ version: 0.3.5
+usb-creator:
+ description: Ubuntu startup disk creator
+ homepage_uri: UNKNOWN
+ name: usb-creator
+ version: 0.2.23
+variant_tools:
+ description: 'Variant tools: an integrated annotation and analysis package for next-gen
+ sequencing data'
+ homepage_uri: http://varianttools.sourceforge.net
+ name: variant_tools
+ version: 1.0.1a
+vboxapi:
+ description: Python interface to VirtualBox
+ homepage_uri: http://www.virtualbox.org
+ name: vboxapi
+ version: '1.0'
+virtualenv:
+ description: Virtual Python Environment builder
+ homepage_uri: http://www.virtualenv.org
+ name: virtualenv
+ version: 1.7.1.2
+wadllib:
+ description: Navigate HTTP resources using WADL files as guides.
+ homepage_uri: https://launchpad.net/wadllib
+ name: wadllib
+ version: 1.3.0
+workerpool:
+ description: Module for distributing jobs to a pool of worker threads.
+ homepage_uri: http://code.google.com/p/workerpool/
+ name: workerpool
+ version: 0.9.2
+wsgiref:
+ description: WSGI (PEP 333) Reference Library
+ homepage_uri: ''
+ name: wsgiref
+ version: 0.1.2
+wxPython:
+ description: Cross platform GUI toolkit for Python
+ homepage_uri: http://wxPython.org/
+ name: wxPython
+ version: 2.8.12.1
+wxPython-common:
+ description: Cross platform GUI toolkit for Python
+ homepage_uri: http://wxPython.org/
+ name: wxPython-common
+ version: 2.8.12.1
+xdiagnose:
+ description: Analysis tools for troubleshooting X.org problems
+ homepage_uri: http://launchpad.net/xdiagnose
+ name: xdiagnose
+ version: '2.5'
+xkit:
+ description: library for the manipulation of the xorg.conf
+ homepage_uri: https://launchpad.net/x-kit
+ name: xkit
+ version: 0.0.0
+xlrd:
+ description: Library for developers to extract data from Microsoft Excel (tm) spreadsheet
+ files
+ homepage_uri: http://www.lexicon.net/sjmachin/xlrd.htm
+ name: xlrd
+ version: 0.7.8
+yolk:
+ description: Command-line tool for querying PyPI and Python packages installed on
+ your system.
+ homepage_uri: https://github.com/cakebread/yolk
+ name: yolk
+ version: 0.4.3
+zope.interface:
+ description: Interfaces for Python
+ homepage_uri: http://pypi.python.org/pypi/zope.interface
+ name: zope.interface
+ version: 3.6.1
View
1,275 manifest/r-packages.yaml
@@ -0,0 +1,1275 @@
+AnnotationDbi:
+ description: Annotation Database Interface
+ homepage_uri: ''
+ name: AnnotationDbi
+ version: 1.18.1
+ArrayExpress:
+ description: 'Access the ArrayExpress Microarray Database at EBI and build\nBioconductor
+ data structures: ExpressionSet, AffyBatch,\nNChannelSet'
+ homepage_uri: ''
+ name: ArrayExpress
+ version: 1.16.0
+ArrayTools:
+ description: geneChip Analysis Package
+ homepage_uri: ''
+ name: ArrayTools
+ version: 1.16.0
+BSgenome:
+ description: Infrastructure for Biostrings-based genome data packages
+ homepage_uri: ''
+ name: BSgenome
+ version: 1.24.0
+BSgenome.Ecoli.NCBI.20080805:
+ description: Escherichia coli full genomes
+ homepage_uri: ''
+ name: BSgenome.Ecoli.NCBI.20080805
+ version: 1.3.17
+BSgenome.Scerevisiae.UCSC.sacCer2:
+ description: Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer2)
+ homepage_uri: ''
+ name: BSgenome.Scerevisiae.UCSC.sacCer2
+ version: 1.3.17
+BayesPeak:
+ description: Bayesian Analysis of ChIP-seq Data
+ homepage_uri: ''
+ name: BayesPeak
+ version: 1.8.0
+BeadDataPackR:
+ description: Compression of Illumina BeadArray data
+ homepage_uri: ''
+ name: BeadDataPackR
+ version: 1.8.0
+BiasedUrn:
+ description: Biased Urn model distributions
+ homepage_uri: http://www.agner.org/random/ http://www.r-project.org
+ name: BiasedUrn
+ version: '1.04'
+Biobase:
+ description: 'Biobase: Base functions for Bioconductor'
+ homepage_uri: ''
+ name: Biobase
+ version: 2.16.0
+BiocGenerics:
+ description: Generic functions for Bioconductor
+ homepage_uri: ''
+ name: BiocGenerics
+ version: 0.2.0
+BiocInstaller:
+ description: Install/Update Bioconductor and CRAN Packages
+ homepage_uri: ''
+ name: BiocInstaller
+ version: 1.4.6
+BiodiversityR:
+ description: GUI for biodiversity and community ecology analysis
+ homepage_uri: http://www.r-project.org,\nhttp://www.worldagroforestry.org/resources/databases/tree-diversity-analysis
+ name: BiodiversityR
+ version: '1.6'
+Biostrings:
+ description: String objects representing biological sequences, and matching\nalgorithms
+ homepage_uri: ''
+ name: Biostrings
+ version: 2.24.1
+CNAnorm:
+ description: A normalization method for Copy Number Aberration in cancer\nsamples
+ homepage_uri: http://www.r-project.org,
+ name: CNAnorm
+ version: 1.2.0
+CSAR:
+ description: Statistical tools for the analysis of ChIP-seq data
+ homepage_uri: ''
+ name: CSAR
+ version: 1.8.0
+Cairo:
+ description: R graphics device using cairo graphics library for creating\nhigh-quality
+ bitmap (PNG, JPEG, TIFF), vector (PDF, SVG,\nPostScript) and display (X11 and
+ Win32) output.
+ homepage_uri: http://www.rforge.net/Cairo/
+ name: Cairo
+ version: 1.5-1
+Category:
+ description: Category Analysis
+ homepage_uri: ''
+ name: Category
+ version: 2.22.0
+ChIPpeakAnno:
+ description: Batch annotation of the peaks identified from either ChIP-seq,\nChIP-chip
+ experiments or any experiments resulted in large\nnumber of chromosome ranges.
+ homepage_uri: ''
+ name: ChIPpeakAnno
+ version: 2.4.0
+ChIPseqR:
+ description: Identifying Protein Binding Sites in High-Throughput Sequencing\nData
+ homepage_uri: ''
+ name: ChIPseqR
+ version: 1.10.0
+ChIPsim:
+ description: Simulation of ChIP-seq experiments
+ homepage_uri: ''
+ name: ChIPsim
+ version: 1.10.0
+DBI:
+ description: R Database Interface
+ homepage_uri: ''
+ name: DBI
+ version: 0.2-5
+DEGseq:
+ description: Identify Differentially Expressed Genes from RNA-seq data
+ homepage_uri: ''
+ name: DEGseq
+ version: 1.10.0
+DESeq:
+ description: Differential gene expression analysis based on the negative\nbinomial
+ distribution
+ homepage_uri: http://www-huber.embl.de/users/anders/DESeq
+ name: DESeq
+ version: 1.8.3
+DEXSeq:
+ description: Inference of differential exon usage in RNA-Seq
+ homepage_uri: ''
+ name: DEXSeq
+ version: 1.2.0
+DNAcopy:
+ description: DNA copy number data analysis
+ homepage_uri: ''
+ name: DNAcopy
+ version: 1.30.0
+DiffBind:
+ description: Differential Binding Analysis of ChIP-Seq peak data
+ homepage_uri: ''
+ name: DiffBind
+ version: 1.2.0
+DynDoc:
+ description: Dynamic document tools
+ homepage_uri: ''
+ name: DynDoc
+ version: 1.34.0
+EDASeq:
+ description: Exploratory Data Analysis and Normalization for RNA-Seq
+ homepage_uri: ''
+ name: EDASeq
+ version: 1.2.0
+GEOquery:
+ description: Get data from NCBI Gene Expression Omnibus (GEO)
+ homepage_uri: http://watson.nci.nih.gov/~sdavis
+ name: GEOquery
+ version: 2.23.5
+GGBase:
+ description: GGBase infrastructure for genetics of gene expression package\nGGtools
+ homepage_uri: ''
+ name: GGBase
+ version: 3.18.0
+GGtools:
+ description: software and data for analyses in genetics of gene expression
+ homepage_uri: ''
+ name: GGtools
+ version: 4.4.0
+GO.db:
+ description: A set of annotation maps describing the entire Gene Ontology
+ homepage_uri: ''
+ name: GO.db
+ version: 2.7.1
+GOFunction:
+ description: 'GO-function: deriving biologcially relevant functions from\nstatistically
+ significant functions'
+ homepage_uri: ''
+ name: GOFunction
+ version: 1.2.0
+GOstats:
+ description: Tools for manipulating GO and microarrays.
+ homepage_uri: ''
+ name: GOstats
+ version: 2.22.0
+GSEABase:
+ description: Gene set enrichment data structures and methods
+ homepage_uri: ''
+ name: GSEABase
+ version: 1.18.0
+GWASExactHW:
+ description: Exact Hardy-Weinburg testing for Genome Wide Association Studies
+ homepage_uri: ''
+ name: GWASExactHW
+ version: '1.0'
+GenomicFeatures:
+ description: Tools for making and manipulating transcript centric annotations
+ homepage_uri: ''
+ name: GenomicFeatures
+ version: 1.8.1
+GenomicRanges:
+ description: Representation and manipulation of genomic intervals
+ homepage_uri: ''
+ name: GenomicRanges
+ version: 1.8.6
+HH:
+ description: 'Statistical Analysis and Data Display: Heiberger and Holland'
+ homepage_uri: ''
+ name: HH
+ version: 2.3-15
+HilbertVis:
+ description: Hilbert curve visualization
+ homepage_uri: http://www.ebi.ac.uk/~anders/hilbert
+ name: HilbertVis
+ version: 1.14.0
+Hmisc:
+ description: Harrell Miscellaneous
+ homepage_uri: http://biostat.mc.vanderbilt.edu/wiki/Main/Hmisc,\nhttp://biostat.mc.vanderbilt.edu/trac/Hmisc
+ name: Hmisc
+ version: 3.9-3
+IRanges:
+ description: Infrastructure for manipulating intervals on sequences
+ homepage_uri: ''
+ name: IRanges
+ version: 1.14.3
+Iso:
+ description: Functions to perform isotonic regression.
+ homepage_uri: http://www.math.unb.ca/~rolf/
+ name: Iso
+ version: 0.0-10
+KEGG.db:
+ description: A set of annotation maps for KEGG
+ homepage_uri: ''
+ name: KEGG.db
+ version: 2.7.1
+KernSmooth:
+ description: Functions for kernel smoothing for Wand & Jones (1995)
+ homepage_uri: ''
+ name: KernSmooth
+ version: 2.23-7
+LowRankQP:
+ description: Low Rank Quadratic Programming
+ homepage_uri: ''
+ name: LowRankQP
+ version: 1.0.1
+MASS:
+ description: Support Functions and Datasets for Venables and Ripley's MASS
+ homepage_uri: http://www.stats.ox.ac.uk/pub/MASS4/
+ name: MASS
+ version: 7.3-18
+MEDIPS:
+ description: MeDIP-Seq data analysis
+ homepage_uri: ''
+ name: MEDIPS
+ version: 1.6.0
+Matrix:
+ description: Sparse and Dense Matrix Classes and Methods
+ homepage_uri: http://Matrix.R-forge.R-project.org/
+ name: Matrix
+ version: 1.0-7
+MotIV:
+ description: Motif Identification and Validation
+ homepage_uri: ''
+ name: MotIV
+ version: 1.10.0
+NMF:
+ description: Algorithms and framework for Nonnegative Matrix Factorization\n(NMF).
+ homepage_uri: http://nmf.r-forge.r-project.org
+ name: NMF
+ version: 0.5.06
+PICS:
+ description: Probabilistic inference of ChIP-seq
+ homepage_uri: ''
+ name: PICS
+ version: 1.10.0
+R.methodsS3:
+ description: Utility function for defining S3 methods
+ homepage_uri: http://www.braju.com/R/
+ name: R.methodsS3
+ version: 1.2.2
+R2HTML:
+ description: HTML exportation for R objects
+ homepage_uri: http://www.r-project.org
+ name: R2HTML
+ version: '2.2'
+R453Plus1Toolbox:
+ description: A package for importing and analyzing data from Roche's Genome\nSequencer
+ System.
+ homepage_uri: ''
+ name: R453Plus1Toolbox
+ version: 1.6.1
+RBGL:
+ description: An interface to the BOOST graph library
+ homepage_uri: http://www.bioconductor.org
+ name: RBGL
+ version: 1.32.0
+RColorBrewer:
+ description: ColorBrewer palettes
+ homepage_uri: ''
+ name: RColorBrewer
+ version: 1.0-5
+RCurl:
+ description: General network (HTTP/FTP/...) client interface for R
+ homepage_uri: http://www.omegahat.org/RCurl
+ name: RCurl
+ version: 1.91-1
+RMySQL:
+ description: R interface to the MySQL database
+ homepage_uri: http://biostat.mc.vanderbilt.edu/RMySQL,\nhttps://github.com/jeffreyhorner/RMySQL
+ name: RMySQL
+ version: 0.9-3
+RSQLite:
+ description: SQLite interface for R
+ homepage_uri: ''
+ name: RSQLite
+ version: 0.11.1
+RSQLite.extfuns:
+ description: Math and String Extension Functions for RSQLite
+ homepage_uri: http://www.sqlite.org/contrib/
+ name: RSQLite.extfuns
+ version: 0.0.1
+Rcpp:
+ description: Seamless R and C++ Integration
+ homepage_uri: http://dirk.eddelbuettel.com/code/rcpp.html,\nhttp://romainfrancois.blog.free.fr/index.php?category/R-package/Rcpp
+ name: Rcpp
+ version: 0.9.10
+Rgraphviz:
+ description: Provides plotting capabilities for R graph objects
+ homepage_uri: ''
+ name: Rgraphviz
+ version: 1.34.1
+Rmpi:
+ description: Interface (Wrapper) to MPI (Message-Passing Interface)
+ homepage_uri: http://www.stats.uwo.ca/faculty/yu/Rmpi
+ name: Rmpi
+ version: 0.5-9
+Rolexa:
+ description: Statistical analysis of Solexa sequencing data
+ homepage_uri: ''
+ name: Rolexa
+ version: 1.12.0
+Rsamtools:
+ description: Binary alignment (BAM), variant call (BCF), or tabix file import
+ homepage_uri: http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
+ name: Rsamtools
+ version: 1.8.5
+SRAdb:
+ description: A compilation of metadata from NCBI SRA and tools
+ homepage_uri: http://watson.nci.nih.gov/
+ name: SRAdb
+ version: 1.10.0
+SVGAnnotation:
+ description: Tools for post-processing SVG plots created in R
+ homepage_uri: ''
+ name: SVGAnnotation
+ version: 0.9-0
+ShortRead:
+ description: Classes and methods for high-throughput short-read sequencing\ndata.
+ homepage_uri: ''
+ name: ShortRead
+ version: 1.14.4
+SparseM:
+ description: Sparse Linear Algebra
+ homepage_uri: http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html
+ name: SparseM
+ version: '0.96'
+TeachingDemos:
+ description: Demonstrations for teaching and learning
+ homepage_uri: ''
+ name: TeachingDemos
+ version: '2.8'
+VariantAnnotation:
+ description: Annotation of Genetic Variants
+ homepage_uri: ''
+ name: VariantAnnotation
+ version: 1.2.8
+XML:
+ description: Tools for parsing and generating XML within R and S-Plus.
+ homepage_uri: http://www.omegahat.org/RSXML
+ name: XML
+ version: 3.9-4
+abind:
+ description: Combine multi-dimensional arrays
+ homepage_uri: ''
+ name: abind
+ version: 1.4-0
+affy:
+ description: Methods for Affymetrix Oligonucleotide Arrays
+ homepage_uri: ''
+ name: affy
+ version: 1.34.0
+affyPLM:
+ description: Methods for fitting probe-level models
+ homepage_uri: http://bmbolstad.com
+ name: affyPLM
+ version: 1.32.0
+affyQCReport:
+ description: QC Report Generation for affyBatch objects
+ homepage_uri: ''
+ name: affyQCReport
+ version: 1.34.0
+affydata:
+ description: Affymetrix Data for Demonstration Purpose
+ homepage_uri: ''
+ name: affydata
+ version: 1.11.16
+affyio:
+ description: Tools for parsing Affymetrix data files
+ homepage_uri: ''
+ name: affyio
+ version: 1.24.0
+affylmGUI:
+ description: GUI for affy analysis using limma package
+ homepage_uri: http://bioinf.wehi.edu.au/affylmGUI/
+ name: affylmGUI
+ version: 1.30.0
+akima:
+ description: Interpolation of irregularly spaced data
+ homepage_uri: ''
+ name: akima
+ version: 0.5-7
+amap:
+ description: Another Multidimensional Analysis Package
+ homepage_uri: http://mulcyber.toulouse.inra.fr/projects/amap/
+ name: amap
+ version: 0.8-7
+annaffy:
+ description: Annotation tools for Affymetrix biological metadata
+ homepage_uri: ''
+ name: annaffy
+ version: 1.28.0
+annotate:
+ description: Annotation for microarrays
+ homepage_uri: ''
+ name: annotate
+ version: 1.34.0
+ape:
+ description: Analyses of Phylogenetics and Evolution
+ homepage_uri: http://ape.mpl.ird.fr/
+ name: ape
+ version: 3.0-4
+aplpack:
+ description: 'Another Plot PACKage: stem.leaf, bagplot, faces, spin3R, and\nsome
+ slider functions'
+ homepage_uri: http://www.wiwi.uni-bielefeld.de/com/wolf/software/aplpack.html
+ name: aplpack
+ version: 1.2.6
+aroma.light:
+ description: Light-weight methods for normalization and visualization of\nmicroarray
+ data using only basic R data types
+ homepage_uri: http://www.aroma-project.org/
+ name: aroma.light
+ version: 1.24.0
+arrayQualityMetrics:
+ description: Quality metrics on microarray data sets
+ homepage_uri: ''
+ name: arrayQualityMetrics
+ version: 3.12.0
+ash:
+ description: David Scott's ASH routines
+ homepage_uri: ''
+ name: ash
+ version: 1.0-13
+base:
+ description: The R Base Package
+ homepage_uri: ''
+ name: base
+ version: 2.15.0
+baySeq:
+ description: Empirical Bayesian analysis of patterns of differential\nexpression
+ in count data
+ homepage_uri: ''
+ name: baySeq
+ version: 1.10.0
+beadarray:
+ description: Quality assessment and low-level analysis for Illumina BeadArray\ndata
+ homepage_uri: ''
+ name: beadarray
+ version: 2.6.0
+biglm:
+ description: bounded memory linear and generalized linear models
+ homepage_uri: ''
+ name: biglm
+ version: '0.8'
+bigmemory:
+ description: Manage massive matrices with shared memory and memory-mapped\nfiles
+ homepage_uri: http://www.bigmemory.org
+ name: bigmemory
+ version: 4.2.11
+bioDist:
+ description: Different distance measures
+ homepage_uri: ''
+ name: bioDist
+ version: 1.28.0
+biomaRt:
+ description: Interface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase\nand
+ Gramene)
+ homepage_uri: ''
+ name: biomaRt
+ version: 2.12.0
+bit:
+ description: A class for vectors of 1-bit booleans
+ homepage_uri: http://ff.r-forge.r-project.org/
+ name: bit
+ version: 1.1-8
+bitops:
+ description: Functions for Bitwise operations
+ homepage_uri: ''
+ name: bitops
+ version: 1.0-4.1
+boot:
+ description: Bootstrap Functions (originally by Angelo Canty for S)
+ homepage_uri: ''
+ name: boot
+ version: 1.3-4
+caTools:
+ description: 'Tools: moving window statistics, GIF, Base64, ROC AUC, etc.'
+ homepage_uri: ''
+ name: caTools
+ version: '1.13'
+car:
+ description: Companion to Applied Regression
+ homepage_uri: https://r-forge.r-project.org/projects/car/,\nhttp://CRAN.R-project.org/package=car,\nhttp://socserv.socsci.mcmaster.ca/jfox/Books/Companion/index.html
+ name: car
+ version: 2.0-12
+chipseq:
+ description: 'chipseq: A package for analyzing chipseq data'
+ homepage_uri: ''
+ name: chipseq
+ version: 1.6.0
+chron:
+ description: Chronological objects which can handle dates and times
+ homepage_uri: ''
+ name: chron
+ version: 2.3-42
+class:
+ description: Functions for Classification
+ homepage_uri: http://www.stats.ox.ac.uk/pub/MASS4/
+ name: class
+ version: 7.3-3
+cluster:
+ description: Cluster Analysis Extended Rousseeuw et al.
+ homepage_uri: ''
+ name: cluster
+ version: 1.14.2
+cn.mops:
+ description: cn.mops - Mixture of Poissons for CNV detection in NGS data
+ homepage_uri: http://www.bioinf.jku.at/software/cnmops/cnmops.html
+ name: cn.mops
+ version: 1.2.5
+codetools:
+ description: Code Analysis Tools for R
+ homepage_uri: ''
+ name: codetools
+ version: 0.2-8
+coin:
+ description: Conditional Inference Procedures in a Permutation Test Framework
+ homepage_uri: ''
+ name: coin
+ version: 1.0-21
+colorspace:
+ description: Color Space Manipulation
+ homepage_uri: ''
+ name: colorspace
+ version: 1.1-1
+compiler:
+ description: The R Compiler Package
+ homepage_uri: ''
+ name: compiler
+ version: 2.15.0
+cummeRbund:
+ description: Analysis, exploration, manipulation, and visualization of\nCufflinks
+ high-throughput sequencing data.
+ homepage_uri: ''
+ name: cummeRbund
+ version: 1.2.0
+datasets:
+ description: The R Datasets Package
+ homepage_uri: ''
+ name: datasets
+ version: 2.15.0
+date:
+ description: Functions for handling dates
+ homepage_uri: ''
+ name: date
+ version: 1.2-32
+devtools:
+ description: Tools to make developing R code easier
+ homepage_uri: ''
+ name: devtools
+ version: '0.6'
+dichromat:
+ description: Color schemes for dichromats
+ homepage_uri: ''
+ name: dichromat
+ version: 1.2-4
+digest:
+ description: Create cryptographic hash digests of R objects
+ homepage_uri: http://dirk.eddelbuettel.com/code/digest.html
+ name: digest
+ version: 0.5.2
+edgeR:
+ description: Empirical analysis of digital gene expression data in R
+ homepage_uri: ''
+ name: edgeR
+ version: 2.6.7
+effects:
+ description: Effect Displays for Linear, Generalized Linear,\nMultinomial-Logit,
+ Proportional-Odds Logit Models and\nMixed-Effects Models
+ homepage_uri: http://www.r-project.org, http://socserv.socsci.mcmaster.ca/jfox/
+ name: effects
+ version: 2.1-1
+evaluate:
+ description: Parsing and evaluation tools that provide more details than the\ndefault.
+ homepage_uri: ''
+ name: evaluate
+ version: 0.4.2
+exomeCopy:
+ description: CNV detection from exome sequencing read depth
+ homepage_uri: ''
+ name: exomeCopy
+ version: 1.2.0
+fBasics:
+ description: Rmetrics - Markets and Basic Statistics
+ homepage_uri: http://www.rmetrics.org
+ name: fBasics
+ version: '2160.81'
+ff:
+ description: memory-efficient storage of large data on disk and fast access\nfunctions
+ homepage_uri: http://ff.r-forge.r-project.org/
+ name: ff
+ version: 2.2-7
+flashClust:
+ description: Implementation of optimal hierarchical clustering
+ homepage_uri: ''
+ name: flashClust
+ version: 1.01-1
+foreign:
+ description: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase,\n...
+ homepage_uri: ''
+ name: foreign
+ version: 0.8-50
+formatR:
+ description: Format R Code Automatically
+ homepage_uri: https://github.com/yihui/formatR/wiki
+ name: formatR
+ version: '0.4'
+gage:
+ description: Generally Applicable Gene-set Enrichment for Pathway Analysis
+ homepage_uri: http://www.biomedcentral.com/1471-2105/10/161
+ name: gage
+ version: 2.6.0
+gcrma:
+ description: Background Adjustment Using Sequence Information
+ homepage_uri: ''
+ name: gcrma
+ version: 2.28.0
+gdata:
+ description: Various R programming tools for data manipulation
+ homepage_uri: ''
+ name: gdata
+ version: 2.10.6
+gee:
+ description: Generalized Estimation Equation solver
+ homepage_uri: ''
+ name: gee
+ version: 4.13-18
+geneLenDataBase:
+ description: Lengths of mRNA transcripts for a number of genomes
+ homepage_uri: ''
+ name: geneLenDataBase
+ version: 0.99.9
+genefilter:
+ description: 'genefilter: methods for filtering genes from microarray\nexperiments'
+ homepage_uri: ''
+ name: genefilter
+ version: 1.38.0
+geneplotter:
+ description: Graphics related functions for Bioconductor
+ homepage_uri: ''
+ name: geneplotter
+ version: 1.34.0
+genomeIntervals:
+ description: Operations on genomic intervals
+ homepage_uri: ''
+ name: genomeIntervals
+ version: 1.12.0
+genoset:
+ description: Provides classes similar to ExpressionSet for copy number\nanalysis
+ homepage_uri: ''
+ name: genoset
+ version: 1.6.0
+ggplot2:
+ description: An implementation of the Grammar of Graphics
+ homepage_uri: http://had.co.nz/ggplot2/
+ name: ggplot2
+ version: 0.9.1
+girafe:
+ description: Genome Intervals and Read Alignments for Functional Exploration
+ homepage_uri: ''
+ name: girafe
+ version: 1.8.0
+globaltest:
+ description: Testing groups of covariates/features for association with a\nresponse
+ variable, with applications to gene set testing
+ homepage_uri: http://www.msbi.nl/goeman
+ name: globaltest
+ version: 5.10.0
+goseq:
+ description: Gene Ontology analyser for RNA-seq and other length biased data
+ homepage_uri: ''
+ name: goseq
+ version: 1.8.0
+gplots:
+ description: Various R programming tools for plotting data
+ homepage_uri: ''
+ name: gplots
+ version: 2.11.0
+grDevices:
+ description: The R Graphics Devices and Support for Colours and Fonts
+ homepage_uri: ''
+ name: grDevices
+ version: 2.15.0
+graph:
+ description: 'graph: A package to handle graph data structures'
+ homepage_uri: ''
+ name: graph
+ version: 1.34.0
+graphics:
+ description: The R Graphics Package
+ homepage_uri: ''
+ name: graphics
+ version: 2.15.0
+grid:
+ description: The Grid Graphics Package
+ homepage_uri: ''
+ name: grid
+ version: 2.15.0
+gsubfn:
+ description: Utilities for strings and function arguments.
+ homepage_uri: http://gsubfn.googlecode.com
+ name: gsubfn
+ version: 0.6-3
+gtools:
+ description: Various R programming tools
+ homepage_uri: ''
+ name: gtools
+ version: 2.6.2
+hdf5:
+ description: HDF5
+ homepage_uri: ''
+ name: hdf5
+ version: 1.6.9
+hdrcde:
+ description: Highest density regions and conditional density estimation
+ homepage_uri: http://www.robjhyndman.com/software/hdrcde
+ name: hdrcde
+ version: '2.16'
+hexbin:
+ description: Hexagonal Binning Routines
+ homepage_uri: ''
+ name: hexbin
+ version: 1.26.0
+hgu95av2.db:
+ description: Affymetrix Human Genome U95 Set annotation data (chip hgu95av2)
+ homepage_uri: ''
+ name: hgu95av2.db
+ version: 2.7.1
+highlight:
+ description: Syntax highlighter
+ homepage_uri: http://r-forge.r-project.org/projects/highlight/,\nhttp://romainfrancois.blog.free.fr/index.php?category/R-package/highlight
+ name: highlight
+ version: 0.3.1
+htSeqTools:
+ description: Quality Control, Visualization and Processing for\nHigh-Throughput
+ Sequencing data
+ homepage_uri: ''
+ name: htSeqTools
+ version: 1.2.0
+hwriter:
+ description: HTML Writer - Outputs R objects in HTML format
+ homepage_uri: http://www.embl.de/~gpau/hwriter/
+ name: hwriter
+ version: '1.3'
+impute:
+ description: 'impute: Imputation for microarray data'
+ homepage_uri: ''
+ name: impute
+ version: 1.30.0
+intervals:
+ description: Tools for working with points and intervals
+ homepage_uri: ''
+ name: intervals
+ version: 0.13.3
+kernlab:
+ description: Kernel-based Machine Learning Lab
+ homepage_uri: ''
+ name: kernlab
+ version: 0.9-14
+knitr:
+ description: A general-purpose package for dynamic report generation in R
+ homepage_uri: http://yihui.name/knitr/
+ name: knitr
+ version: '0.6'
+ks:
+ description: Kernel smoothing
+ homepage_uri: http://www.mvstat.net/tduong
+ name: ks
+ version: 1.8.8
+labeling:
+ description: Axis Labeling
+ homepage_uri: ''
+ name: labeling
+ version: '0.1'
+lattice:
+ description: Lattice Graphics
+ homepage_uri: http://lattice.r-forge.r-project.org/
+ name: lattice
+ version: 0.20-6
+latticeExtra:
+ description: Extra Graphical Utilities Based on Lattice
+ homepage_uri: http://latticeextra.r-forge.r-project.org/
+ name: latticeExtra
+ version: 0.6-19
+leaps:
+ description: regression subset selection
+ homepage_uri: ''
+ name: leaps
+ version: '2.9'
+limSolve:
+ description: Solving Linear Inverse Models
+ homepage_uri: ''
+ name: limSolve
+ version: 1.5.3
+limma:
+ description: Linear Models for Microarray Data
+ homepage_uri: http://bioinf.wehi.edu.au/limma
+ name: limma
+ version: 3.12.1
+lmtest:
+ description: Testing Linear Regression Models
+ homepage_uri: ''
+ name: lmtest
+ version: 0.9-30
+locfit:
+ description: Local Regression, Likelihood and Density Estimation.
+ homepage_uri: ''
+ name: locfit
+ version: 1.5-8
+lpSolve:
+ description: Interface to Lp_solve v. 5.5 to solve linear/integer programs
+ homepage_uri: ''
+ name: lpSolve
+ version: 5.6.6
+lumi:
+ description: BeadArray Specific Methods for Illumina Methylation and\nExpression
+ Microarrays
+ homepage_uri: ''
+ name: lumi
+ version: 2.8.0
+makecdfenv:
+ description: CDF Environment Maker
+ homepage_uri: ''
+ name: makecdfenv
+ version: 1.34.0
+maptree:
+ description: Mapping, pruning, and graphing tree models
+ homepage_uri: http://www.epa.gov/wed/pages/staff/white/
+ name: maptree
+ version: 1.4-6
+markdown:
+ description: Markdown rendering for R
+ homepage_uri: ''
+ name: markdown
+ version: 0.5.1
+marray:
+ description: Exploratory analysis for two-color spotted microarray data
+ homepage_uri: http://www.maths.usyd.edu.au/u/jeany/
+ name: marray
+ version: 1.34.0
+matrixStats:
+ description: Methods that apply to rows and columns of a matrix
+ homepage_uri: ''
+ name: matrixStats
+ version: 0.5.0
+mclust:
+ description: Model-Based Clustering / Normal Mixture Modeling
+ homepage_uri: http://www.stat.washington.edu/research/reports/2006/tr504.pdf
+ name: mclust
+ version: 3.4.11
+memoise:
+ description: Memoise functions
+ homepage_uri: ''
+ name: memoise
+ version: '0.1'
+methods:
+ description: Formal Methods and Classes
+ homepage_uri: ''
+ name: methods
+ version: 2.15.0
+methylumi:
+ description: Handle Illumina methylation data
+ homepage_uri: ''
+ name: methylumi
+ version: 2.2.0
+mgcv:
+ description: Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness\nestimation
+ homepage_uri: ''
+ name: mgcv
+ version: 1.7-18
+misc3d:
+ description: Miscellaneous 3D Plots
+ homepage_uri: ''
+ name: misc3d
+ version: 0.8-2
+modeltools:
+ description: Tools and Classes for Statistical Models
+ homepage_uri: ''
+ name: modeltools
+ version: 0.2-19
+multcomp:
+ description: Simultaneous Inference in General Parametric Models
+ homepage_uri: The publishers web page is\nhttp://www.crcpress.com/product/isbn/9781584885740
+ name: multcomp
+ version: 1.2-12
+multicore:
+ description: Parallel processing of R code on machines with multiple cores or\nCPUs
+ homepage_uri: http://www.rforge.net/multicore/
+ name: multicore
+ version: 0.1-7
+multtest:
+ description: Resampling-based multiple hypothesis testing
+ homepage_uri: ''
+ name: multtest
+ version: 2.12.0
+munsell:
+ description: Munsell colour system
+ homepage_uri: ''
+ name: munsell
+ version: '0.3'
+mvtnorm:
+ description: Multivariate Normal and t Distributions
+ homepage_uri: ''
+ name: mvtnorm
+ version: 0.9-9992
+nleqslv:
+ description: Solve systems of non linear equations
+ homepage_uri: ''
+ name: nleqslv
+ version: 1.9.3
+nlme:
+ description: Linear and Nonlinear Mixed Effects Models
+ homepage_uri: ''
+ name: nlme
+ version: 3.1-104
+nnet:
+ description: Feed-forward Neural Networks and Multinomial Log-Linear Models
+ homepage_uri: http://www.stats.ox.ac.uk/pub/MASS4/
+ name: nnet
+ version: 7.3-1
+numDeriv:
+ description: Accurate Numerical Derivatives
+ homepage_uri: http:http://optimizer.r-forge.r-project.org/
+ name: numDeriv
+ version: 2012.3-1
+oneChannelGUI:
+ description: A graphical interface designed to facilitate analysis of\nmicroarrays
+ and miRNA/RNA-seq data on laptops.
+ homepage_uri: http://www.bioinformatica.unito.it/oneChannelGUI/
+ name: oneChannelGUI
+ version: 1.22.7
+org.Hs.eg.db:
+ description: Genome wide annotation for Human
+ homepage_uri: ''
+ name: org.Hs.eg.db
+ version: 2.7.1
+pamr:
+ description: 'Pam: prediction analysis for microarrays'
+ homepage_uri: ''
+ name: pamr
+ version: '1.54'
+parallel:
+ description: Support for Parallel computation in R
+ homepage_uri: ''
+ name: parallel
+ version: 2.15.0
+parser:
+ description: Detailed R source code parser
+ homepage_uri: http://www.r-enthusiasts.com
+ name: parser
+ version: 0.0-14
+permute:
+ description: Functions for generating restricted permutations of data
+ homepage_uri: http://vegan.r-forge.r-project.org/
+ name: permute
+ version: 0.7-0
+pi0:
+ description: Estimating the proportion of true null hypotheses for FDR
+ homepage_uri: ''
+ name: pi0
+ version: 1.3-200
+plotrix:
+ description: Various plotting functions
+ homepage_uri: ''
+ name: plotrix
+ version: 3.4-1
+plyr:
+ description: Tools for splitting, applying and combining data
+ homepage_uri: http://had.co.nz/plyr
+ name: plyr
+ version: 1.7.1
+preprocessCore:
+ description: A collection of pre-processing functions
+ homepage_uri: ''
+ name: preprocessCore
+ version: 1.18.0
+proto:
+ description: Prototype object-based programming
+ homepage_uri: http://r-proto.googlecode.com
+ name: proto
+ version: 0.3-9.2
+quadprog:
+ description: Functions to solve Quadratic Programming Problems.
+ homepage_uri: ''
+ name: quadprog
+ version: 1.5-4
+qvalue:
+ description: Q-value estimation for false discovery rate control
+ homepage_uri: ''
+ name: qvalue
+ version: 1.30.0
+rGADEM:
+ description: de novo motif discovery
+ homepage_uri: ''
+ name: rGADEM
+ version: 2.4.0
+relimp:
+ description: Relative Contribution of Effects in a Regression Model
+ homepage_uri: http://go.warwick.ac.uk/relimp, http://go.warwick.ac.uk/dfirth
+ name: relimp
+ version: 1.0-3
+reshape:
+ description: Flexibly reshape data.
+ homepage_uri: http://had.co.nz/reshape
+ name: reshape
+ version: 0.8.4
+reshape2:
+ description: 'Flexibly reshape data: a reboot of the reshape package.'
+ homepage_uri: http://had.co.nz/reshape
+ name: reshape2
+ version: 1.2.1
+rgl:
+ description: 3D visualization device system (OpenGL)
+ homepage_uri: http://rgl.neoscientists.org
+ name: rgl
+ version: 0.92.880
+rjson:
+ description: JSON for R
+ homepage_uri: ''
+ name: rjson
+ version: 0.2.8
+rnaSeqMap:
+ description: rnaSeq secondary analyses
+ homepage_uri: ''
+ name: rnaSeqMap
+ version: 2.10.0
+rpart:
+ description: Recursive Partitioning
+ homepage_uri: \nhttp://mayoresearch.mayo.edu/mayo/research/biostat/splusfunctions.cfm
+ name: rpart
+ version: 3.1-53
+rtracklayer:
+ description: R interface to genome browsers and their annotation tracks
+ homepage_uri: ''
+ name: rtracklayer
+ version: 1.16.1
+samr:
+ description: 'SAM: Significance Analysis of Microarrays'
+ homepage_uri: http://www-stat.stanford.edu/~tibs/SAM
+ name: samr
+ version: '2.0'
+sandwich:
+ description: Robust Covariance Matrix Estimators
+ homepage_uri: ''
+ name: sandwich
+ version: 2.2-9
+scales:
+ description: Scale functions for graphics.
+ homepage_uri: ''
+ name: scales
+ version: 0.2.1
+scatterplot3d:
+ description: 3D Scatter Plot
+ homepage_uri: ''
+ name: scatterplot3d
+ version: 0.3-33
+segmentSeq:
+ description: Methods for identifying small RNA loci from high-throughput\nsequencing
+ data
+ homepage_uri: ''
+ name: segmentSeq
+ version: 1.8.0
+seqLogo:
+ description: Sequence logos for DNA sequence alignments
+ homepage_uri: ''
+ name: seqLogo
+ version: 1.22.0
+setRNG:
+ description: Set (Normal) Random Number Generator and Seed
+ homepage_uri: http://distr.r-forge.r-project.org/
+ name: setRNG
+ version: 2011.11-2
+siggenes:
+ description: Multiple testing using SAM and Efron's empirical Bayes\napproaches
+ homepage_uri: ''
+ name: siggenes
+ version: 1.30.0
+simpleaffy:
+ description: Very simple high level analysis of Affymetrix data
+ homepage_uri: http://www.bioconductor.org,\nhttp://bioinformatics.picr.man.ac.uk/simpleaffy/
+ name: simpleaffy
+ version: 2.32.0
+sm:
+ description: Smoothing methods for nonparametric regression and density\nestimation
+ homepage_uri: http://www.stats.gla.ac.uk/~adrian/sm
+ name: sm
+ version: 2.2-4.1
+snow:
+ description: Simple Network of Workstations
+ homepage_uri: ''
+ name: snow
+ version: 0.3-9
+snowfall:
+ description: Easier cluster computing (based on snow).
+ homepage_uri: ''
+ name: snowfall
+ version: '1.84'
+snpStats:
+ description: SnpMatrix and XSnpMatrix classes and methods
+ homepage_uri: http://www-gene.cimr.cam.ac.uk/clayton
+ name: snpStats
+ version: 1.6.0
+spatial:
+ description: Functions for Kriging and Point Pattern Analysis
+ homepage_uri: http://www.stats.ox.ac.uk/pub/MASS4/
+ name: spatial
+ version: 7.3-3
+splines:
+ description: Regression Spline Functions and Classes
+ homepage_uri: ''
+ name: splines
+ version: 2.15.0
+splots:
+ description: Visualization of high-throughput assays in microtitre plate or\nslide
+ format
+ homepage_uri: ''
+ name: splots
+ version: 1.22.0
+sqldf:
+ description: Perform SQL Selects on R Data Frames
+ homepage_uri: http://sqldf.googlecode.com
+ name: sqldf
+ version: 0.4-6.4
+stabledist:
+ description: Stable Distribution Functions
+ homepage_uri: http://www.rmetrics.org
+ name: stabledist
+ version: 0.6-4
+statmod:
+ description: Statistical Modeling
+ homepage_uri: http://www.statsci.org/r
+ name: statmod
+ version: 1.4.14
+stats:
+ description: The R Stats Package
+ homepage_uri: ''
+ name: stats
+ version: 2.15.0
+stats4:
+ description: Statistical Functions using S4 Classes
+ homepage_uri: ''
+ name: stats4
+ version: 2.15.0
+stringr:
+ description: Make it easier to work with strings.
+ homepage_uri: ''
+ name: stringr
+ version: '0.6'
+strucchange:
+ description: Testing, Monitoring, and Dating Structural Changes
+ homepage_uri: ''
+ name: strucchange
+ version: 1.4-7
+survival:
+ description: Survival analysis, including penalised likelihood.
+ homepage_uri: http://r-forge.r-project.org
+ name: survival
+ version: 2.36-14
+tcltk:
+ description: Tcl/Tk Interface
+ homepage_uri: ''
+ name: tcltk
+ version: 2.15.0
+timeDate:
+ description: Rmetrics - Chronological and Calendarical Objects
+ homepage_uri: http://www.rmetrics.org
+ name: timeDate
+ version: '2160.95'
+timeSeries:
+ description: Rmetrics - Financial Time Series Objects
+ homepage_uri: http://www.rmetrics.org
+ name: timeSeries
+ version: '2160.94'
+timsac:
+ description: TIMe Series Analysis and Control package
+ homepage_uri: ''
+ name: timsac
+ version: 1.2.7
+tkWidgets:
+ description: R based tk widgets