Package: scregclust 0.2.0

Felix Held

scregclust: Reconstructing the Regulatory Programs of Target Genes in scRNA-Seq Data

Implementation of the scregclust algorithm described in Larsson, Held, et al. (2024) <doi:10.1038/s41467-024-53954-3> which reconstructs regulatory programs of target genes in scRNA-seq data. Target genes are clustered into modules and each module is associated with a linear model describing the regulatory program.

Authors:Felix Held [aut, cre], Ida Larsson [aut], Sven Nelander [aut], André Armatowski [ctb]

scregclust_0.2.0.tar.gz
scregclust_0.2.0.tar.gz(r-4.5-noble)scregclust_0.2.0.tar.gz(r-4.4-noble)
scregclust_0.2.0.tgz(r-4.4-emscripten)scregclust_0.2.0.tgz(r-4.3-emscripten)
scregclust.pdf |scregclust.html
scregclust/json (API)
NEWS

# Install 'scregclust' in R:
install.packages('scregclust', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/scmethods/scregclust/issues

Pkgdown:https://scmethods.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

cppopenmp

3.48 score 30 scripts 287 downloads 15 exports 35 dependencies

Last updated 2 days agofrom:2ed974f82d. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 06 2024
R-4.5-linux-x86_64OKDec 06 2024

Exports:available_resultscluster_overlapfast_corfind_module_sizesget_avg_num_regulatorsget_num_final_configsget_rand_indicesget_regulator_listget_target_gene_moduleskmeansppplot_module_count_helperplot_regulator_networkplot_silhouettesscregclustscregclust_format

Dependencies:clicolorspacecpp11fansifarverggplot2gluegtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrprettyunitsR6RColorBrewerRcppRcppEigenreshaperlangscalestibbleutf8vctrsviridisLitewithr

Demonstration of workflow

Rendered frompbmc.Rmdusingknitr::rmarkdownon Dec 06 2024.

Last update: 2024-12-06
Started: 2024-11-21