Man pages for vitkl/regNETcmap
Tools to study transcriptional regulation using perturbation screens followed by transcriptomic profiling (incl. CMAP, Perturb-seq)

completeCellGeneCombsFind cell lines and perturbations (Connectivity map) where...
findOrthologsmap orthologous genes using ENSEMBL BioMART
geneName2PerturbAnnoGet Connectivity Map perturbation annotations for genes of...
ks.test_explsimulation and plots explaining KS-test and Wilcox-test
loadCMapLoad Connectivity Map project data (1st and 2nd phase, Level...
mapIDsMap moleculer identifiers using ENSEMBL BioMart
measureTrPheMeasuring mutually exclusive transcriptional phenotypes
openCellInfoRead connectivity map annotations
perturbTableSummarise available perturbation data annotations using...
plotTFtargetsINcmapPlot TF perturbation effects (CMap) on TF targets
readCMAPRead Connectivity Map data given perturbation annotations
readCMAPsubsetRead a subsets of perturbations (Connectivity Map data, all...
regFromCMAPFind regulators of gene sets using Connectivity Map...
showLargestRegulonsShow largest TF regulons
svdCMAPCalculate and remove principal components from Connectivity...
TFtargetsINcmapSummarise TF targets enrichment when TF perturbed in...
vitkl/regNETcmap documentation built on Nov. 19, 2018, 7:56 a.m.