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:10.1186/s13059-019-1874-1>, and Choudhary and Satija (2022) <doi:10.1186/s13059-021-02584-9>
for more details.
| Version: |
0.4.1 |
| Depends: |
R (≥ 3.6.0) |
| Imports: |
dplyr, magrittr, MASS, Matrix (≥ 1.5-0), methods, future.apply, future, ggplot2, reshape2, rlang, gridExtra, matrixStats |
| LinkingTo: |
RcppArmadillo, Rcpp (≥ 0.11.0) |
| Suggests: |
irlba, testthat, knitr |
| Enhances: |
glmGamPoi |
| Published: |
2023-10-19 |
| DOI: |
10.32614/CRAN.package.sctransform |
| Author: |
Christoph Hafemeister
 [aut],
Saket Choudhary
[aut, cre],
Rahul Satija
[ctb] |
| Maintainer: |
Saket Choudhary <schoudhary at nygenome.org> |
| BugReports: |
https://github.com/satijalab/sctransform/issues |
| License: |
GPL-3 | file LICENSE |
| URL: |
https://github.com/satijalab/sctransform |
| NeedsCompilation: |
yes |
| SystemRequirements: |
C++17 |
| Citation: |
sctransform citation info |
| Materials: |
README NEWS |
| CRAN checks: |
sctransform results |
Documentation:
Downloads:
Reverse dependencies:
Linking:
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