Package: sctransform 0.4.1
Saket Choudhary
sctransform: Variance Stabilizing Transformations for Single Cell UMI Data
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.
Authors:
sctransform_0.4.1.tar.gz
sctransform_0.4.1.tar.gz(r-4.5-noble)sctransform_0.4.1.tar.gz(r-4.4-noble)
sctransform_0.4.1.tgz(r-4.4-emscripten)sctransform_0.4.1.tgz(r-4.3-emscripten)
sctransform.pdf |sctransform.html✨
sctransform/json (API)
NEWS
| # Install 'sctransform' in R: |
| install.packages('sctransform', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/satijalab/sctransform/issues
- pbmc - Peripheral Blood Mononuclear Cells
- umify_data - Transformation functions for umify
Last updated 1 years agofrom:de74747424. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 13 2024 |
| R-4.5-linux-x86_64 | OK | Oct 13 2024 |
Exports:correctcorrect_countsdiff_mean_testdiff_mean_test_conservedgenerateget_model_varget_residual_varget_residualsplot_modelplot_model_parssmooth_via_pcaumifyvst
Dependencies:clicodetoolscolorspacedigestdplyrfansifarverfuturefuture.applygenericsggplot2globalsgluegridExtragtableisobandlabelinglatticelifecyclelistenvmagrittrMASSMatrixmatrixStatsmgcvmunsellnlmeparallellypillarpkgconfigplyrR6RColorBrewerRcppRcppArmadilloreshape2rlangscalesstringistringrtibbletidyselectutf8vctrsviridisLitewithr
