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:Christoph Hafemeister [aut], Saket Choudhary [aut, cre], Rahul Satija [ctb]

sctransform_0.4.1.tar.gz
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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'))

Peer review:

Bug tracker:https://github.com/satijalab/sctransform/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • pbmc - Peripheral Blood Mononuclear Cells
  • umify_data - Transformation functions for umify

openblascpp

6.45 score 1 stars 70 packages 1.6k scripts 27k downloads 34 mentions 13 exports 46 dependencies

Last updated 1 years agofrom:de74747424. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 12 2024
R-4.5-linux-x86_64OKDec 12 2024

Exports:correctcorrect_countsdiff_mean_testdiff_mean_test_conservedgenerateget_model_varget_residual_varget_residualsplot_modelplot_model_parssmooth_via_pcaumifyvst

Dependencies:clicodetoolscolorspacedigestdplyrfansifarverfuturefuture.applygenericsggplot2globalsgluegridExtragtableisobandlabelinglatticelifecyclelistenvmagrittrMASSMatrixmatrixStatsmgcvmunsellnlmeparallellypillarpkgconfigplyrR6RColorBrewerRcppRcppArmadilloreshape2rlangscalesstringistringrtibbletidyselectutf8vctrsviridisLitewithr