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sctransform
View on CRAN: Click
here
Download and install sctransform package within the R console
Install from CRAN:
install.packages("sctransform")
Install from Github:
library("remotes")
install_github("cran/sctransform") Install by package version:
library("remotes")
install_version("sctransform", "0.4.3") Attach the package and use:
library("sctransform")
Maintained by
Saket Choudhary
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-11-18
Latest Update: 2025-04-30
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)
, and Choudhary and Satija (2022)
for more details.
How to cite:
Saket Choudhary (2018). sctransform: Variance Stabilizing Transformations for Single Cell UMI Data. R package version 0.4.3, https://cran.r-project.org/web/packages/sctransform. Accessed 10 Oct. 2026.
Previous versions and publish date:
(2026-07-09 07:02), 0.1.0 (2018-11-18 17:30), 0.2.0 (2019-04-12 14:32), 0.2.1 (2019-12-17 16:00), 0.3.1 (2020-10-08 14:00), 0.3.2 (2020-12-16 15:40), 0.3.3 (2022-01-13 09:20), 0.3.4 (2022-08-21 00:10), 0.3.5 (2022-09-21 19:10), 0.3 (2020-09-20 16:40), 0.4.0 (2023-09-19 06:50), 0.4.1 (2023-10-19 06:40), 0.4.2 (2025-04-30 19:20)
Other packages that cited sctransform R package
View sctransform citation profile
Other R packages that sctransform depends,
imports, suggests or enhances
Complete documentation for sctransform
Functions, R codes and Examples using
the sctransform R package
Some associated functions: compare_expression . correct . correct_counts . diff_mean_test . diff_mean_test_conserved . generate . get_model_var . get_nz_median2 . get_residual_var . get_residuals . is_outlier . make.sparse . pbmc . plot_model . plot_model_pars . robust_scale . robust_scale_binned . row_gmean . row_var . smooth_via_pca . umify . umify_data . vst .
Some associated R codes: RcppExports.R . data.R . denoise.R . differential_expression.R . fit.R . generate.R . plotting.R . umify.R . utils.R . vst.R . Full sctransform package functions and examples
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