Download

Latest Release

To install the downloaded package, use:

R CMD INSTALL scde_X.Y.Z.tar.gz

Development Version

Available on Github

To install the development version from Github, use:

require(devtools)
devtools::install_version('flexmix', '2.3-13')
devtools::install_github('hms-dbmi/scde', build_vignettes = FALSE)

Troubleshooting

curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /

scde depends on an older version of the R package flexmix. If you are receiving errors during installation, make sure to install flexmix 2.3-13 first.

require(devtools)
devtools::install_version('flexmix', '2.3-13')

Old Releases

The old release of scde contains functionalities for error modeling and differential expression analysis detailed in "Bayesian approach to single-cell differential expression analysis" (Kharchenko PV, Silberstein L, Scadden DT, Nature Methods, doi:10.1038/nmeth.2967).

• fixed error in posterior mode calculations in scde.posteriors()
• cleaned up package dependencies, removed deprecated multicore dependency
• fixed a bug in scde.browse.diffexp() where it used a global variable
• optimized memory usage during error model construction

• added support for batch bias correction. See scde.expression.difference() and scde.test.gene.expression.difference() help for details
• added a local web browser interface to view differential expression results. See scde.browse.diffexp() help for details.
• added ability to fit models to a reference transcriptome (usually a bulk measurement). See scde.fit.models.to.reference() method for details

• The initial release implements simplified methods for the basic workflow and significantly speeds up differential expression testing.

• This release implements all the basic functionality that is described in the original publication. It uses explicit handling of posterior distributions to test differential expression.