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:
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 = 'https://cloud.r-project.org') |
Bug tracker:https://github.com/scmethods/scregclust/issues
Pkgdown site:https://scmethods.github.io
Last updated 4 months agofrom:2ed974f82d. Checks:2 OK, 1 NOTE. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 06 2025 |
| R-4.5-linux-x86_64 | NOTE | Mar 06 2025 |
| R-4.4-linux-x86_64 | OK | Mar 06 2025 |
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
Citation
Larsson I, Held F, Popova G, Koc A, Kundu S, Jörnsten R, Nelander S (2024). “Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers.” Nature Communications, 15(9699). doi:10.1038/s41467-024-53954-3.
Corresponding BibTeX entry:
@Article{,
title = {Reconstructing the regulatory programs underlying the
phenotypic plasticity of neural cancers},
author = {Ida Larsson and Felix Held and Gergana Popova and Alper
Koc and Soumi Kundu and Rebecka Jörnsten and Sven Nelander},
journal = {Nature Communications},
year = {2024},
volume = {15},
number = {9699},
doi = {10.1038/s41467-024-53954-3},
}
Readme and manuals
Single-cell Regulatory-driven Clustering (scregclust)
The goal of scregclust is to cluster genes by regulatory programs. To do so, genes are clustered into modules which in turn are associated with regulators. The algorithm alternates between associating regulators to modules and reallocating target genes into modules.
- The documentation for this package can be found at https://scmethods.github.io/scregclust/
- A detailed description of the algorithm and an in-depth evaluation of its properties can be found in our original research article Larsson, Held, et al. (2024) Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers. Nature Communications 15, 9699 DOI 10.1038/s41467-024-53954-3
Installation
You can install the stable version of scregclust from CRAN with
install.packages("scregclust")
You can install the current development version of scregclust from GitHub with:
# install.packages("devtools")
devtools::install_github("scmethods/scregclust")
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 |
