Man pages for Japrin/scPip
pipeline for scRNA-seq data analysis
| calEffectSizeFromDE | calculate effect size given a de.out object |
| calProliferationScore | calculate the proliferation score |
| cal.signatureScore.gdT.Fred | Identification of gamma delta T cells (Fred's method) |
| convertLimmaToSCE | convert the limma result to gene by meta-cluster data stored... |
| fill.contamination | calculate the signature score of one potential contaminated... |
| g.geneOnUmap.list | special gene list |
| gset.list | lists of gene sets |
| HVG.From.GeneRankTb | highly variable genes finding (method using percetile rank... |
| inSilico.TCell | Identification of T cells (simple average-threshold method) |
| inSilico.TGammaDelta | Identification of gamma delta T cells (simple... |
| make.geneTableLong | make a long type gene table, given a SingleCellExperiment... |
| mergeDataFromFileTable | merge data file file table |
| mergeSCEDataFromFileTable | collapse gene by cell expression data to gene by mini-cluster... |
| render_KnitReport | render a knitr report |
| resetSig | reset the significance |
| run.HVG | Wraper for highly variable genes finding |
| run.inte.metaClust | run the integration pipeline |
| run.Leiden | wrapper for running leiden clustering |
| run.Scanorama | Wraper for running Scanorama |
| run.scanpy | Wraper for running scanpy pipeline |
| run.Seurat3 | Wraper for running Seurat3 pipeline |
| sigGeneHeatmap | make heatmap for top signature genes |
