sctransform

0.4.3

Variance Stabilizing Transformations for Single Cell UMI Data

4packages depend

583.4Kdownloads / year

22.4%test coverage

13/13checks pass

Overview

About

Maintained by Saket ChoudharyFirst published 2018-11-1813 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("sctransform", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("satijalab/sctransform")

Development version from satijalab/sctransform. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-sctransform

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-sctransform

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-sctransform

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 5.0 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.07

22.4%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 209 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 95%
Return-value docs: 100%
References docs: 0%

Downloads

583.4K

CRAN downloads in the past year

Rank #554 · ~1.6K/day · ~48.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

44.2K30 days

129.1K90 days

583.4K1 year

Compare downloads with other packages →

Also on11.1K r2u1 autocran112.3K conda_forge71 c2d4u

Repository

GitHub ↗ satijalab/sctransform

267Stars

38Forks

49Open issues

0Open PRs

12Releases

311Commits

10Contributors

License GPL-3.0 · 311 commits · Last activity 2026-01-10 · +0.4% stars, 30d

Stars over time

2025-07-29 · 2252026-07-22 · 267

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/satijalab/sctransform on 2026-07-30.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdrevdep/

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (13)

dplyr magrittrMASSMatrixmethodsfuture.apply future parallelly ggplot2 reshape2 rlang gridExtra matrixStats

LinkingTo (2)

RcppArmadillo Rcpp

Suggests (3)

irlba testthat knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

43indirect

Seurat spatialGE RESET VAM

Code & Tests

People & History

People (3)

Maintainer (1)

Saket Choudhary

Author, Maintainer · added in 0.3.3

Authors (2)

Saket Choudhary

Author, Maintainer · added in 0.3.3

Christoph Hafemeister

Author

Contributors (1)

Rahul Satija

Contributor · added in 0.3.3

Package Timeline

13 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.4.3Latest
2026-01-10 · current release · diff ↗
0.4.2
2025-04-30 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.4.1
2023-10-19 · diff ↗
0.4.0
2023-09-19 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.3.5
2022-09-21 · diff ↗
0.3.4
2022-08-21 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.3.3
2022-01-13 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.3.2
2020-12-16 · diff ↗
0.3.1
2020-10-08 · diff ↗
0.3
2020-09-20 · diff ↗

Show 6 earlier events

R
R 4.0.0 released · 2020-04-24
0.2.1
2019-12-17 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.2.0
2019-04-12 · diff ↗
0.1.0
2018-11-18
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-11-18
Total releases: 13 / 8 yrs
License: GPL-3 | file LICENSE OSI
Minimum R: ≥ 3.6.0
Bundled data: 114 KB / 2 files
Download size: 183 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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