Man pages for vitkl/regNETcmap
Tools to study transcriptional regulation using perturbation screens followed by transcriptomic profiling (incl. CMAP, Perturb-seq)
| completeCellGeneCombs | Find cell lines and perturbations (Connectivity map) where... |
| findOrthologs | map orthologous genes using ENSEMBL BioMART |
| geneName2PerturbAnno | Get Connectivity Map perturbation annotations for genes of... |
| ks.test_expl | simulation and plots explaining KS-test and Wilcox-test |
| loadCMap | Load Connectivity Map project data (1st and 2nd phase, Level... |
| mapIDs | Map moleculer identifiers using ENSEMBL BioMart |
| measureTrPhe | Measuring mutually exclusive transcriptional phenotypes |
| openCellInfo | Read connectivity map annotations |
| perturbTable | Summarise available perturbation data annotations using... |
| plotTFtargetsINcmap | Plot TF perturbation effects (CMap) on TF targets |
| readCMAP | Read Connectivity Map data given perturbation annotations |
| readCMAPsubset | Read a subsets of perturbations (Connectivity Map data, all... |
| regFromCMAP | Find regulators of gene sets using Connectivity Map... |
| showLargestRegulons | Show largest TF regulons |
| svdCMAP | Calculate and remove principal components from Connectivity... |
| TFtargetsINcmap | Summarise TF targets enrichment when TF perturbed in... |
