Man pages for zcollest/scRegNetwrapper
Wrapper functions for single cell regulatory network analysis (DoRothEA, PROGENy, pySCENIC) as well as tools for downstream analysis and method comparisons.
| correlation_analysis | Generating a correlation matrix of pathways and TFs |
| custom_pathways_calc | Calculate pathway activity using a dataframe of custom... |
| custom_regulons_calc | Quantifying TF activity using a data frame of custom regulons... |
| downstream_heatmap | Plotting dorothea/progeny scores by comparison group on a... |
| find_associated_pathways | Given a list of genes, find which pathways they are... |
| find_associated_TFs | Given a list of genes, find which TFs they are associated... |
| get_dorothea_regulons | Returning DoRothEA Regulons |
| get_progeny_pathways | Returning PROGENy pathways |
| handle_dorothea_scores | Handling the dorothea scores (proportion adjustments,... |
| handle_progeny_scores | Handling the progeny scores (proportion adjustments,... |
| handle_pyscenic_results | Uses reticulate package to handle and process the results... |
| pathway_effsize_calc | Cohen's D effect size calculation for progeny data (requires... |
| plot_RSS | Uses reticulate package to plot RSS using python |
| pooledSD | Pooled Standard Deviation Calculation |
| reformat_progeny_pathways | Reformat the progeny pathway data when you select only the... |
| run_aucell | Uses reticulate package to run AUCell from R |
| run_cistarget | Uses reticulate package to run CisTarget (regulon prediction)... |
| run_dorothea | Quantifying TF activity from DoRothEA Regulons |
| run_grn | Uses reticulate package to run GRN from R |
| run_loom_setup | Uses reticulate package to set up loom file for pySCENIC... |
| run_progeny | Calculating pathway activity scores from PROGENy pathways |
| tf_effsize_calc | Cohen's D effect size calculation for dorothea data (requires... |
