sctransform
Variance Stabilizing Transformations for Single Cell UMI Data
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) <doi:10.1186/s13059-019-1874-1>, and Choudhary and Satija (2022) <doi:10.1186/s13059-021-02584-9> for more details.
Downloads
40.1K
Last 30 days
569th
150.7K
Last 90 days
577.2K
Last year
Trend: -7.3% (30d vs prior 30d)
914
Last 30 days
3.2K
Last 90 days
10.4K
Last year
Trend: -8.9% (30d vs prior 30d)
0
Last 7 days
7
Last 30 days
0
All-time
autoCRAN-only: this name is served only by autoCRAN, so the count is exact.
CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 25, 2026
NOTE 13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 22, 2026
package dependencies
Package which this enhances but not available for checking: ‘glmGamPoi’
ERROR 12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 18, 2026
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.6/sctransform.Rcheck/00install.out' for details.
package dependencies
Package which this enhances but not available for checking: ‘glmGamPoi’
NOTE 13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
package dependencies
Package which this enhances but not available for checking: ‘glmGamPoi’