Package: scregclust 0.2.5

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_0.2.5.tar.gz
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scregclust_0.2.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scregclust/json (API)
NEWS

# Install 'scregclust' in R:

install.packages('scregclust', repos = c('https://scmethods.r-universe.dev', 'https://cloud.r-project.org'))

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

Pkgdown/docs site:https://scmethods.github.io

Uses libs:

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

On CRAN:

clustering regulatory-programs scrna-seq-analysis cpp openmp

5.05 score 14 stars 20 scripts 500 downloads 15 exports 27 dependencies

Last updated from:ee69d147be. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	235
linux-devel-x86_64	OK	245
source / vignettes	OK	264
linux-release-arm64	OK	217
linux-release-x86_64	OK	227
macos-release-arm64	OK	175
macos-release-x86_64	OK	312
macos-oldrel-arm64	OK	210
macos-oldrel-x86_64	OK	280
windows-devel	OK	187
windows-release	OK	186
windows-oldrel	OK	225
wasm-release	OK	205

Exports:available_results cluster_overlap fast_cor find_module_sizes get_avg_num_regulators get_num_final_configs get_rand_indices get_regulator_list get_target_gene_modules kmeanspp plot_module_count_helper plot_regulator_network plot_silhouettes scregclust scregclust_format

Dependencies:cli cpp11 farver ggplot2 glue gtable igraph isoband labeling lattice lifecycle magrittr Matrix pkgconfig plyr prettyunits R6 RColorBrewer Rcpp RcppEigen reshape rlang S7 scales vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Extract final configurations into a data frame	available_results
Create a table of module overlap for two clusterings	cluster_overlap
Fast computation of correlation	fast_cor
Determine module sizes	find_module_sizes
Get the average number of active regulators per module	get_avg_num_regulators
Return the number of final configurations	get_num_final_configs
Compute Rand indices	get_rand_indices
Return list of regulator genes	get_regulator_list
Extract target gene modules for given penalization parameters	get_target_gene_modules
Perform the k-means++ algorithm	kmeanspp
Plot average silhouette scores and average predictive R^2	plot_module_count_helper
Plotting the regulatory table from scregclust as a directed graph	plot_regulator_network
Plot individual silhouette scores	plot_silhouettes
Uncover gene modules and their regulatory programs from single-cell data	scregclust
Package data before clustering	scregclust_format