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‎DESCRIPTION‎

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Package: sctransform
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Type: Package
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Title: Variance Stabilizing Transformations for Single Cell UMI Data
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Version: 0.4.1.9002
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Version: 0.4.1.9003
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Date: 2025-04-30
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Authors@R: c(
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person(given = "Christoph", family = "Hafemeister", email = "christoph.hafemeister@nyu.edu", role = "aut", comment = c(ORCID = "0000-0001-6365-8254")),
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person(given = "Saket", family = "Choudhary", email = "schoudhary@nygenome.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5202-7633")),
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person(given = "Saket", family = "Choudhary", email = "saketc@iitb.ac.in", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5202-7633")),
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person(given = "Rahul", family = "Satija", email = "rsatija@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-9448-8833"))
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)
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Description: A normalization method for single-cell UMI count data using a

‎README.md‎

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```r
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# Runnning sctransform on a UMI matrix
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normalized_data <- sctransform::vst(umi_count_matrix)$y
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# v2 regularization
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normalized_data <- sctransform::vst(umi_count_matrix, vst.flavor="v2")$y
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# v1 regularization
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normalized_data <- sctransform::vst(umi_count_matrix, vst.flavor="v1")$y
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# Runnning sctransform on a Seurat object
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seurat_object <- Seurat::SCTransform(seurat_object)
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#v2 regularization
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seurat_object <- Seurat::SCTransform(seurat_object, vst.flavor="v2")
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# v1 regularization
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seurat_object <- Seurat::SCTransform(seurat_object, vst.flavor="v1")
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```
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## Help
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- [Variance stabilizing transformation](https://htmlpreview.github.io/?https://github.com/satijalab/sctransform/blob/supp_html/supplement/variance_stabilizing_transformation.html)
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- [Using sctransform in Seurat](https://htmlpreview.github.io/?https://github.com/satijalab/sctransform/blob/supp_html/supplement/seurat.html)
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- [Examples of how to perform normalization, feature selection, integration, and differential expression with sctransform v2 regularization](https://satijalab.org/seurat/articles/sctransform_v2_vignette.html)
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- [Examples of how to perform normalization, feature selection, integration, and differential expression with sctransform v2 regularization](https://satijalab.org/seurat/articles/sctransform_vignette)
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Please use [the issue tracker](https://github.com/satijalab/sctransform/issues) if you encounter a problem

‎revdep/README.md‎

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# Platform
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|field |value |
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|:--------|:----------------------------------------------|
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|version |R version 4.3.1 (2023-06-16) |
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|os |Ubuntu 20.04.6 LTS |
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|system |x86_64, linux-gnu |
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|ui |RStudio |
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|language |(EN) |
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|collate |en_US.UTF-8 |
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|ctype |en_US.UTF-8 |
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|tz |America/New_York |
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|date |2023-09-18 |
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|rstudio |2023.03.1+446 Cherry Blossom (server) |
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|pandoc |3.1.3 @ /home/choudharys/miniconda3/bin/pandoc |
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|field |value |
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|:--------|:-------------------------------------------------------------|
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|version |R version 4.5.0 (2025-04-11) |
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|os |Ubuntu 24.04.2 LTS |
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|system |x86_64, linux-gnu |
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|ui |RStudio |
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|language |en_GB:en |
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|collate |en_GB.UTF-8 |
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|ctype |en_GB.UTF-8 |
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|tz |Asia/Kolkata |
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|date |2025-04-30 |
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|rstudio |2024.12.1+563 Kousa Dogwood (desktop) |
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|pandoc |3.6.4 @ /data/miniconda3/bin/pandoc |
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|quarto |1.5.57 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/quarto |
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# Dependencies
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|package |old |new |Δ |
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|:-------------|:-----|:----------|:--|
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|sctransform |0.3.5 |0.4.0 |* |
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|digest |NA |0.6.33 |* |
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|dplyr |NA |1.1.3 |* |
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|future |NA |1.33.0 |* |
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|future.apply |NA |1.11.0 |* |
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|ggplot2 |NA |3.4.3 |* |
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|gtable |NA |0.3.4 |* |
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|labeling |NA |0.4.3 |* |
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|matrixStats |NA |1.0.0 |* |
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|parallelly |NA |1.36.0 |* |
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|Rcpp |NA |1.0.11 |* |
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|RcppArmadillo |NA |0.12.6.4.0 |* |
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|rlang |NA |1.1.1 |* |
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|vctrs |NA |0.6.3 |* |
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|viridisLite |NA |0.4.2 |* |
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|package |old |new |Δ |
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|:-----------|:---|:----------|:--|
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|sctransform |NA |0.4.1.9003 |* |
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# Revdeps
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## Failed to check (6)
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## Failed to check (7)
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|package |version |error |warning |note |
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|:-------|:-------|:-----|:-------|:----|
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|CAMML |? | | | |
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|EWCE |? | | | |
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|muscat |? | | | |
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|RESET |? | | | |
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|Seurat |? | | | |
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|VAM |? | | | |
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|package |version |error |warning |note |
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|:--------|:-------|:-----|:-------|:----|
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|CAMML |? | | | |
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|EWCE |? | | | |
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|muscat |? | | | |
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|RESET |? | | | |
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|SCdeconR |? | | | |
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|Seurat |? | | | |
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|VAM |? | | | |
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‎revdep/cran.md‎

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## revdepcheck results
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We checked 6 reverse dependencies (0 from CRAN + 6 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
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We checked 7 reverse dependencies (0 from CRAN + 7 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
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* We saw 0 new problems
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* We failed to check 0 packages

‎revdep/failures.md‎

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```
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# SCdeconR
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<details>
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* Version:
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* GitHub: https://github.com/satijalab/sctransform
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* Source code: NA
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* Number of recursive dependencies: 0
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</details>
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## Error before installation
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### Devel
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```
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```
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### CRAN
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```
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```
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# Seurat
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