Single-Cell RNA-Seq Gene Expression Recovery
An implementation of a regularized regression prediction and
empirical Bayes method to recover the true gene expression profile in
noisy and sparse single-cell RNA-seq data. See Huang M, et al (2018)
<10.1038> for more details.10.1038>
SAVER (Single-cell Analysis Via Expression Recovery) implements a regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse single-cell RNA-seq data.
You can install the most recent updates of SAVER from github with:
To install the stable release of SAVER:
For more information about the method, check out the website, tutorial, and paper.
SAVER 1.1.1 (September 26, 2018)
- Fix bug when inputted mu values are far from observed
get.mu function to get prior mean predictions.
SAVER 1.1.0 (September 2, 2018)
- Improve finish time estimation
- Allow input of prior predictions
- Can set
ncores to set up parallel backend
- Update documentation
- Make SAVER tutorial vignette
- Allow input of sparse matrices
- Allow return of estimates matrix only
SAVER 1.0.0 (April 25, 2018)
SAVER 0.4.0 (February 28, 2018)
- Implemented faster version of SAVER which is 20-30x faster
- No longer necessary to specify
- Implemented progress bar
SAVER 0.3.1 (January 29, 2018)
- Implement mean expression cutoff for prediction matrix
- Fix minor bugs
SAVER 0.3.0 (September 19, 2017)
- Combine parallel output using
unlist instead of
Reduce is computationally intensive. Might cause issue #1.
- Add nlambda option to
SAVER 0.2.2 (August 13, 2017)
- Rewrote combine function of parallel implementation of
- Add null model option to
SAVER 0.2.1 (August 1, 2017)
- Rewrote parallel implementation of SAVER
- Added verbose, pred.cells, and predict.time options to
SAVER 0.2.0 (July 23, 2017)
- Addressed issue #1
- Add option to filter genes out for prediction in
- Created correlation adjustment functions
SAVER 0.1.3 (July 18, 2017)
- Addressed issue #1
- Remove requirement of
- More accurate calculation of finish time
- Update version number
SAVER 0.1.2 (May 29, 2017)
sample.saver to sample datasets from the posterior distribution.
- Documented dataset and package.
- Included size factor, number of genes and cells, and names to
SAVER 0.1.1 (May 9, 2017)
Prerelease version with documentation.