Man pages for yanwu2014/perturbLM
A lightweight R package that uses linear models to analyze the effects of chemical/genetic perturbations, conditions, and disease states on single gene expression.
| AvgGroupExpr | Compute average (scaled) expression of cells in each group |
| CalcClusterEnrich | Calculate cluster enrichment with logistic regression |
| CalcClusterEnrichPvals | Calculate cluster enrichment with logistic regression |
| CalcGeneModuleEffect | Calculate effect of perturbations on gene modules |
| CalcGlmnet | Calculate penalized linear regression with glmnet |
| CalcGlmnetPvals | Calculate regression coefficients and p-values via... |
| CleanControls | Remove all cells in the control perturbation(s) that also... |
| CleanDesignCtrl | Filters out cells that belong to control genotype and other... |
| ClusterWiseDE | Compute per-cluster differential expression between... |
| computeEMD | Visualize correlation between two vectors. Adapted from PhEMD... |
| CreateDesignMatrix | Convert perturbation dictionary to design matrix |
| cross_entropy | Helper function for computing cross entropy |
| cross_validate_lambda | Helper function for running cross validation on a sequence of... |
| CurateData | Curate perturbation dataset (in Seurat object format) |
| DesignMatrixGenotypes | Convert genotypes list to design matrix.... |
| EvaluateLinearModel | Function for evaluating linear model performance |
| ExtractField | Extract a field from a delimited string |
| FastRead | Efficiently load tabular datasets using data.table |
| FilterGenesets | Filter genesets by minimum, maximum number of genes |
| FisherEnrich | Use Fisher's exact test to calculate enrichment for count... |
| FlattenGroups | Convert list of sample groups into a flat vector. Removes all... |
| GetCoefMatrix | Extract coefficient matrix from a multigaussian glmnet object |
| GroupClusterComp | Get cluster composition of each perturbation |
| GroupClusterCounts | Counts the number of cells in each perturbation/cluster |
| GroupOverlapCounts | Counts the number of cells in each group overlap combination |
| hello | Hello, World! |
| LoadGenesets | Read genesets from gmt file to list format |
| MergeGroupLists | Merge two perturbation dicts |
| MergeGroups | Merge perturbations with the same pattern in names. For... |
| MultipleFisherEnrich | Count over-enrichment for a list of gene markers |
| MultipleGSEAEnrich | GSEA over-enrichment test using liger |
| PlotBox | Boxplot of features |
| PlotClusterComp | Plot cluster compositions |
| PlotCorrelation | Visualize correlation between two vectors |
| PlotHexBin | Visualize correlation between two vectors with density plot.... |
| PlotResiduals | Plot predicted values vs residuals to assess data linearity... |
| PredictMixedLM | Predict expression given a new model dataframe |
| ReadGroups | Read in sample groups from a csv file format |
| RunCrossValidation | Run cross validation for both alpha and lambda |
| RunLinearModel | Wrapper function for running a ElasticNet model on a single... |
| RunMixedLM | Run per-gene linear mixed models using glmmLasso |
| SetupLinearModel | Set up design matrices and response given a Seurat object |
| SplitFoldsByGroup | Splits data into folds stratified by a perturbation... |
| StratifyGroupList | Stratify groups by additional factor |
| UnflattenGroups | Converts a flat sample groups character vector into a list... |
| Write10X | Write sparse matrix using the 10X file format |
| WriteGenesets | Write genesets from list to gmt file |
| WriteGroups | Write sample groups from list to csv format |
