Package: scregclust 0.1.10
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_0.1.10.tar.gz
scregclust_0.1.10.tar.gz(r-4.5-noble)scregclust_0.1.10.tar.gz(r-4.4-noble)
scregclust_0.1.10.tgz(r-4.4-emscripten)scregclust_0.1.10.tgz(r-4.3-emscripten)
scregclust.pdf |scregclust.html✨
scregclust/json (API)
| # Install 'scregclust' in R: |
| install.packages('scregclust', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/scmethods/scregclust/issues
Last updated 5 days agofrom:11510136f3. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 25 2024 |
| R-4.5-linux-x86_64 | OK | Nov 25 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
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 |
