Latest Release

Version 1.99.1

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:

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


Installation on Mac OS X may require this additional gfortran library:

curl -O
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.

devtools::install_version('flexmix', '2.3-13')
See the help page for additional support.

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).

Version 1.2.1
Version 1.1
Version 1.0
Version 0.9