sctransform

Variance Stabilizing Transformations for Single Cell UMI Data

A normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As part of the same regression framework, this package also provides functions for batch correction, and data correction. See Hafemeister and Satija 2019 <doi:10.1101/576827> for more details.

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Description file content

Package
sctransform
Type
Package
Title
Variance Stabilizing Transformations for Single Cell UMI Data
Version
0.2.0
Description
A normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As part of the same regression framework, this package also provides functions for batch correction, and data correction. See Hafemeister and Satija 2019 for more details.
URL
BugReports
https://github.com/ChristophH/sctransform/issues
License
GPL-3 | file LICENSE
Encoding
UTF-8
LazyData
true
Depends
R (>= 3.0.2)
Imports
MASS, Matrix, methods, future, future.apply, ggplot2, reshape2, gridExtra, Rcpp
LinkingTo
Rcpp (>= 0.11.0), RcppEigen
Suggests
irlba, testthat
RoxygenNote
6.1.1
NeedsCompilation
yes
Packaged
2019-04-11 23:46:40 UTC; chafemeister
Author
Christoph Hafemeister [aut, cre] ()
Maintainer
Christoph Hafemeister
Repository
CRAN
Date/Publication
2019-04-12 12:32:38 UTC

install.packages('sctransform')

0.2.0

12 days ago

https://github.com/ChristophH/sctransform

Christoph Hafemeister

GPL-3 | file LICENSE

Depends on

R (>= 3.0.2)

Imports

MASS, Matrix, methods, future, future.apply, ggplot2, reshape2, gridExtra, Rcpp

Suggests

irlba, testthat

Discussions