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sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression

https://github.com/satijalab/sctransform

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 11 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 9 committers (11.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.8%) to scientific vocabulary

Keywords from Contributors

human-cell-atlas single-cell-genomics single-cell-rna-seq
Last synced: 9 months ago · JSON representation

Repository

R package for modeling single cell UMI expression data using regularized negative binomial regression

Basic Info
  • Host: GitHub
  • Owner: satijalab
  • License: gpl-3.0
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 20.3 MB
Statistics
  • Stars: 230
  • Watchers: 16
  • Forks: 36
  • Open Issues: 47
  • Releases: 11
Created almost 8 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License

README.md

sctransform

R package for normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

The sctransform package was developed by Christoph Hafemeister in Rahul Satija's lab at the New York Genome Center and described in Hafemeister and Satija, Genome Biology 2019. Recent updates are described in (Choudhary and Satija, Genome Biology, 2022). Core functionality of this package has been integrated into Seurat, an R package designed for QC, analysis, and exploration of single cell RNA-seq data.

Quick start

Installation:

```r

Install sctransform from CRAN

install.packages("sctransform")

Or the development version from GitHub:

remotes::install_github("satijalab/sctransform", ref="develop") ```

Running sctransform:

```r

Runnning sctransform on a UMI matrix

normalizeddata <- sctransform::vst(umicount_matrix)$y

v1 regularization

normalizeddata <- sctransform::vst(umicount_matrix, vst.flavor="v1")$y

Runnning sctransform on a Seurat object

seuratobject <- Seurat::SCTransform(seuratobject)

v1 regularization

seuratobject <- Seurat::SCTransform(seuratobject, vst.flavor="v1") ```

Help

For usage examples see vignettes in inst/doc or use the built-in help after installation
?sctransform::vst

Available vignettes:

Please use the issue tracker if you encounter a problem

References

Owner

  • Name: satijalab
  • Login: satijalab
  • Kind: organization

GitHub Events

Total
  • Create event: 1
  • Release event: 1
  • Issues event: 10
  • Watch event: 19
  • Issue comment event: 15
  • Push event: 6
  • Pull request event: 2
  • Fork event: 5
Last Year
  • Create event: 1
  • Release event: 1
  • Issues event: 10
  • Watch event: 19
  • Issue comment event: 15
  • Push event: 6
  • Pull request event: 2
  • Fork event: 5

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 286
  • Total Committers: 9
  • Avg Commits per committer: 31.778
  • Development Distribution Score (DDS): 0.531
Past Year
  • Commits: 6
  • Committers: 1
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Christoph Hafemeister c****r@n****u 134
Christoph Hafemeister c****r@n****g 96
Saket Choudhary s****c@g****m 48
rsatija s****l@g****m 3
moi-taiga 8****a 1
Diego H d****o@g****m 1
AustinHartman h****9@g****m 1
Andrew Butler a****r@n****g 1
Aiden Grossman a****4@y****m 1
Committer Domains (Top 20 + Academic)
nygenome.org: 2 nyu.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 131
  • Total pull requests: 8
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 27 days
  • Total issue authors: 118
  • Total pull request authors: 6
  • Average comments per issue: 2.58
  • Average comments per pull request: 0.88
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 8
  • Pull requests: 1
  • Average time to close issues: 10 days
  • Average time to close pull requests: about 9 hours
  • Issue authors: 8
  • Pull request authors: 1
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ScreachingFire (3)
  • lucygarner (3)
  • ElyasMo (2)
  • z5ouyang (2)
  • PilanEli (2)
  • duocang (2)
  • yesitsjess (2)
  • Evenlyeven (2)
  • HelloWorldLTY (2)
  • kmwinkley (2)
  • reneemoerkens (2)
  • winner0809 (2)
  • frederikziebell (2)
  • lima1 (1)
  • HillJamie (1)
Pull Request Authors
  • saketkc (4)
  • dieghernan (2)
  • boomanaiden154 (1)
  • kmwinkley (1)
  • rsatija (1)
  • moi-taiga (1)
Top Labels
Issue Labels
more-information-needed (2)
Pull Request Labels

Packages

  • Total packages: 3
  • Total downloads:
    • cran 36,949 last-month
  • Total docker downloads: 159,359
  • Total dependent packages: 7
    (may contain duplicates)
  • Total dependent repositories: 36
    (may contain duplicates)
  • Total versions: 31
  • Total maintainers: 1
proxy.golang.org: github.com/satijalab/sctransform
  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 10 months ago
cran.r-project.org: sctransform

Variance Stabilizing Transformations for Single Cell UMI Data

  • Versions: 12
  • Dependent Packages: 5
  • Dependent Repositories: 33
  • Downloads: 36,949 Last month
  • Docker Downloads: 159,359
Rankings
Downloads: 2.1%
Forks count: 2.2%
Stargazers count: 2.3%
Dependent repos count: 4.6%
Average: 6.2%
Dependent packages count: 8.2%
Docker downloads count: 17.7%
Maintainers (1)
saketc@iitb.ac.in
Last synced: 10 months ago
conda-forge.org: r-sctransform
  • Versions: 8
  • Dependent Packages: 2
  • Dependent Repositories: 3
Rankings
Dependent repos count: 18.0%
Dependent packages count: 19.6%
Average: 23.6%
Stargazers count: 27.3%
Forks count: 29.4%
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • glmGamPoi * enhances
  • MASS * imports
  • Matrix >= 1.5.0 imports
  • dplyr * imports
  • future * imports
  • future.apply * imports
  • ggplot2 * imports
  • gridExtra * imports
  • magrittr * imports
  • matrixStats * imports
  • methods * imports
  • reshape2 * imports
  • rlang * imports
  • irlba * suggests
  • knitr * suggests
  • testthat * suggests