Man pages for yanwu2014/perturbLM
Analyzes effect of genetic perturbations on the transcriptome using a linear model. Based on the MIMOSCA python package (

CalcClusterEnrichCalculate cluster enrichment with logistic regression
CalcClusterEnrichPvalsCalculate cluster enrichment with logistic regression
CalcGeneModuleEffectCalculate effect of perturbations on gene modules
CalcGlmnetCalculate penalized linear regression with glmnet
CalcGlmnetPvalsCalculate regression coefficients and p-values via...
CleanDesignCtrlFilters out cells that belong to control genotype and other...
DesignMatrixGenotypesConvert genotypes list to design matrix
FilterGenesetsFilter genesets by minimum, maximum number of genes
FisherEnrichUse Fisher's exact test to calculate enrichment for count...
FlattenGenotypeListConvert genotypes dictionary from list to named vector. All...
GenesetDotPlotDot plot visualization
GenotypeClusterCountsCounts the number of cells in each genotype x cluster...
GenotypeClusterPvalsUse Fisher's exact test to calculate enrichment for each...
GetCoefMatrixExtract coefficient matrix from a multigaussian glmnet object
ggBarplotMake simple barplot from vector
helloHello, World!
LoadGenesetsRead genesets from gmt file to list format
MultipleFisherEnrichCount over-enrichment for a list of gene markers
MultipleGSEAEnrichGSEA over-enrichment test using liger
PadDesignMatrixPad design matrix with zeros for cells without a called...
PlotCorrelationVisualize correlation between two vectors
PlotHexBinVisualize correlation between two vectors with density plot....
PlotViolinViolin plot (adapted from Seurat)
ReadGenotypesRead in genotypes dictionary from csv file. Returns an R...
UnflattenCellGenotypesConvert genotypes from named vector to list
WriteGenesetsWrite genesets from list to gmt file
WriteGenotypesWrite genotypes to csv file
yanwu2014/perturbLM documentation built on Oct. 27, 2018, 6:58 a.m.