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myCRAN repository |
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Installation
Packages from this repository can be installed via the following call in an R session:# get biocLite from bioconductor
source('http://bioconductor.org/biocLite.R')
# or
library(BiocInstaller)
# Example: install NMF package
# On Windows or Mac OS X, this will try install the source package
# if a binary package is not available for the OS version
biocLite('NMF', siteRepos=c('http://web.cbio.uct.ac.za/~renaud/CRAN'), type='both')
Please contribute Mac packages!
I do not have access to a Mac, so I welcome "donations" of Mac binary version of the packages available on this repository. You can build a binary package and email me the package (See build instructions ).- Download a source package from: http://web.cbio.uct.ac.za/~renaud/CRAN/src/contrib/
- Open a shell and type the following commands:
# wget http://web.cbio.uct.ac.za/~renaud/CRAN/src/contrib/pkg_1.0.tar.gz mkdir tmplib R CMD INSTALL -l tmplib --build pkg_1.0.tar.gz
where "pkg_1.0.tar.gz" corresponds to the version of the source package you want to build. - Email me the newly built package -- with extension ".tgz" -- at , mentionning which version of Mac OS X you used
Packages
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CellMix - A Comprehensive Toolbox for Gene Expression Deconvolution - Details [Version 1.6.2]
This package contains methods and utilities for performing gene expression deconvolution, i.e. estimating cell type proportions and/or cell-specific gene expression signatures from global expression data in heterogeneous samples. One of its central objectives is to provide a unified and user-friendly interface to easily run such analyses.
Author: Renaud Gaujoux, Cathal Seoighe
Maintainer: Renaud Gaujoux
Source: CellMix_1.6.2.tar.gz
Documentation: Man pages
Vignettes:
Depends:R (>= 3.0), methods, pkgmaker (>= 0.16), NMF (>= 0.14), csSAM (>= 1.2.4), registry, stats, stringr, GSEABase, Biobase
Imports:graphics, BiocGenerics, annotate, matrixStats (>= 0.10), genefilter, AnnotationDbi, RSQLite, DBI, preprocessCore, limSolve, quadprog, corpcor, xtable, gtools, csSAM, beeswarm, graph, BiocInstaller, bibtex, digest, ggplot2, plyr
Suggests:RUnit, lumi, hgu133a.db, hgu133b.db, hgu133plus2.db, illuminaHumanv2.db, rat2302.db, hom.Hs.inp.db, GEOmetadb, xlsx, GEOquery (>= 2.26.1), ArrayExpress (>= 1.20.0), biomaRt, knitr
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dbutils - Database Utility Functions - Details [Version 1.1.0]
More about what it does (maybe more than one line)
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux
Source: dbutils_1.1.0.tar.gz
Depends:R (>= 3.0)
Imports:utils, DBI
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deconf - decomposition (deconfounding) of OMICS datasets in heterogeneous tissues - Details [Version 1.0.1]
Decomposition of OMICS data M (e.g. genes by samples) into M = S*C, S: genes by cell types, C: cell types by samples
Author: Dirk Repsilber, Anna Telaar
Maintainer: Dirk Repsilber
Source: deconf_1.0.1.tar.gz / Windows: deconf_1.0.1.zip [R-3.0]
Depends:R (>= 2.10), corpcor
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NMF - Algorithms and framework for Nonnegative Matrix Factorization (NMF) - Details [Version 0.20]
This package provides a framework to perform Non-negative Matrix Factorization (NMF). It implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.
Author: Renaud Gaujoux, Cathal Seoighe
Maintainer: Renaud Gaujoux
Source: NMF_0.20.tar.gz / Windows: NMF_0.20.zip [R-3.0]
Documentation: Man pages
Vignettes:
Depends:R (>= 3.0.0), methods, utils, pkgmaker (>= 0.17.4), registry, rngtools (>= 1.2.3), cluster
Imports:graphics, stats, stringr, digest, grid, grDevices, gridBase, colorspace, RColorBrewer, foreach, doParallel, ggplot2, reshape2
Suggests:RcppOctave (>= 0.11), fastICA, doMPI, bigmemory (>= 4.2), synchronicity, corpcor, xtable, devtools, knitr, bibtex, RUnit, mail, Biobase
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NMFged - Semi-Supervised Nonnegative Matrix Factorization for Gene Expression Deconvolution - Details [Version 1.0]
This package implements an approach that incorporates prior knowledge from marker genes into NMF algorithms, in order to improve the consistency with which both cell type proportions and cell type gene expression signatures are estimated. It provides algorithms and utilities to reproduce the results presented in: "Semi-Supervised Nonnegative Matrix Factorization for Gene Expression Deconvolution: a Case Study", Renaud Gaujoux, Cathal Seoighe (2011), Journal of MEEGID IMPORTANT: This package is not supported any more, as it is superseded by the CellMix package, which incorporates all its functionalities, and much more...
Author: Renaud Gaujoux, Cathal Seoighe
Maintainer: Renaud Gaujoux
Source: NMFged_1.0.tar.gz / Windows: NMFged_1.0.zip [R-2.12] - NMFged_1.0.zip [R-2.13]
Depends:methods, NMF (>= 0.5.99), NMF (<= 0.5.99), colorspace, RColorBrewer, deconf, gridBase, stringr, xtable, Biobase, hgu133plus2.db
Suggests:GEOquery
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pkgmaker - Package development utilities - Details [Version 0.21.1]
This package provides some low-level utilities to use for package development. It currently provides managers for multiple package specific options and registries, vignette, unit test and bibtex related utilities. It serves as a base package for packages like NMF, RcppOctave, doRNG, and as an incubator package for other general purposes utilities, that will eventually be packaged separately. It is still under heavy development and changes in the interface(s) are more than likely to happen.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux
Source: pkgmaker_0.21.1.tar.gz
Depends:R (>= 3.0.0), stats, registry
Imports:methods, tools, codetools, digest, stringr, xtable, grDevices
Suggests:devtools (>= 0.8), bibtex, RUnit, testthat, knitr, ReportingTools, hwriter, argparse
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RcppOctave - Seamless Interface to Octave -- and Matlab - Details [Version 0.13.3]
Direct interface to Octave. The primary goal is to facilitate the port of Matlab/Octave scripts to R. The package enables to call any Octave functions from R and as well as browsing their documentation, passing variables between R and Octave, using R core RNGs in Octave, which ensures that stochastic computations are also reproducible.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux
Source: RcppOctave_0.13.3.tar.gz / Windows: RcppOctave_0.13.3.zip [R-3.0]
Depends:R (>= 3.0.0), methods, utils, stats, Rcpp (>= 0.10.1), pkgmaker (>= 0.17)
Imports:digest, stringr, tools
Suggests:RUnit, knitr, bibtex
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repotools - Tools for R Package Repositories - Details [Version 1.2.2]
Provides utilities to facilitate the creation and usage of CRAN-like repositories.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux
Source: repotools_1.2.2.tar.gz
Depends:R (>= 3.0), pkgmaker (>= 0.22)
Imports:tools, devtools, RCurl
Suggests:BiocInstaller