Packages from this repository can be installed via the following call in an R session:
# get biocLite from bioconductor
# 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
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
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
One of its central objectives is to provide a unified and user-friendly
interface to easily run such analyses.
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.
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
"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IMPORTANT: This package is not supported any more, as it is superseded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...
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.
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.