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) for more details.


Travis-CI Build Status

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.

Installation

You can install the most recent updates of SAVER from github with:

# install.packages("devtools")
devtools::install_github("mohuangx/SAVER")

To install the stable release of SAVER:

# install.packages("devtools")
devtools::install_github("mohuangx/[email protected]*release")

Reference

For more information about the method, check out the website, tutorial, and paper.

News

SAVER 1.1.1 (September 26, 2018)

  • Fix bug when inputted mu values are far from observed
  • Add 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)

  • First official release

SAVER 0.4.0 (February 28, 2018)

  • Implemented faster version of SAVER which is 20-30x faster
  • No longer necessary to specify parallel=TRUE
  • Implemented progress bar

SAVER 0.3.1 (January 29, 2018)

  • Incorporate iterators package
  • 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.
    • Reduce is computationally intensive. Might cause issue #1.
  • Add nlambda option to saver
  • Incorporate bigmemory package
  • Export cor.cells

SAVER 0.2.2 (August 13, 2017)

  • Rewrote combine function of parallel implementation of saver
  • Add null model option to saver

SAVER 0.2.1 (August 1, 2017)

  • Rewrote parallel implementation of SAVER
  • Added verbose, pred.cells, and predict.time options to saver

SAVER 0.2.0 (July 23, 2017)

  • Addressed issue #1
  • Add option to filter genes out for prediction in saver
  • Reduced saver output
  • Created correlation adjustment functions cor.genes and cor.cells

SAVER 0.1.3 (July 18, 2017)

  • Addressed issue #1
  • Remove requirement of saver object
  • Created sample.saver function
  • More accurate calculation of finish time
  • Update version number

SAVER 0.1.2 (May 29, 2017)

  • Added 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 output.
  • Created saver class.

SAVER 0.1.1 (May 9, 2017)

Prerelease version with documentation.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("SAVER")

1.1.1 by Mo Huang, 6 months ago


https://github.com/mohuangx/SAVER


Report a bug at https://github.com/mohuangx/SAVER/issues


Browse source code at https://github.com/cran/SAVER


Authors: Mo Huang [aut, cre] , Nancy Zhang [aut] , Mingyao Li [aut]


Documentation:   PDF Manual  


GPL-2 license


Imports glmnet, foreach, methods, iterators, doParallel, Matrix

Suggests knitr, rmarkdown


See at CRAN