API for minzheguo/SINCERA
An R implementation of SINCERA pipeline for processing single-cell RNA-seq data.
| Global functions | |
|---|---|
| GeneStats | Man page Source code |
| batch.analysis | Man page |
| batch.analysis.ISCCD | Man page Source code |
| batch.analysis.MA | Man page Source code |
| batch.analysis.QQ | Man page Source code |
| celltype.enrichment | Man page |
| celltype.enrichment.initKB | Man page Source code |
| celltype.validation | Man page |
| cluster.assignment | Man page |
| cluster.diffgenes | Man page |
| cluster.geneSelection | Man page |
| cluster.ordering | Man page Source code |
| cluster.permutation.analysis | Man page |
| cluster.permutation.analysis.1 | Man page Source code |
| clustering.consensus | Source code |
| clustering.graph | Source code |
| clustering.hc | Source code |
| clustering.kmeans | Source code |
| clustering.pam | Source code |
| clustering.tight | Source code |
| clusterings.compare | Man page Source code |
| common.helper | Source code |
| consensus_maximization | Man page Source code |
| construct | Man page Source code |
| copyCellMeta | Man page Source code |
| copyGeneMeta | Man page Source code |
| diff.test.samseq | Source code |
| doPCA | Man page |
| doTSNE | Man page |
| drivingforce.getLCC | Man page |
| drivingforce.inferTRN | Man page |
| drivingforce.rankTFs | Man page |
| drivingforce.selectTFs | Man page |
| drivingforce.selectTGs | Man page |
| expr.minimum | Man page |
| exprs.common | Man page Source code |
| exprs.specificity | Man page Source code |
| exprs.synthetic.similarity | Man page Source code |
| exprs.test.statistic.metric | Man page Source code |
| exprs.unique | Man page Source code |
| filterContaminatedCells | Man page |
| filterLowQualityCells | Man page |
| getAssociationTable | Source code |
| getCellMeta | Man page Source code |
| getCellNum | Man page Source code |
| getCellType | Man page Source code |
| getCellTypeEnrichment | Source code |
| getCellTypeMarkers | Man page Source code |
| getCellTypeValidation | Source code |
| getCells | Man page Source code |
| getDF | Source code |
| getDiffGenes | Source code |
| getDiffTest | Source code |
| getES | Source code |
| getExprQuantiles | Man page Source code |
| getExpression | Man page Source code |
| getGeneMeta | Man page Source code |
| getGeneNum | Man page Source code |
| getGenes | Man page Source code |
| getGenesForClustering | Man page Source code |
| getHC | Source code |
| getNodesImportance | Man page Source code |
| getPCA | Man page Source code |
| getPlotDims | Source code |
| getSigGenes | Source code |
| getSigValidation | Source code |
| getTFs | Source code |
| getTSNE | Source code |
| getTimestamp | Source code |
| get_edges | Source code |
| hello | Man page |
| multiplot | Source code |
| network.inference | Man page Source code |
| normalization.log | Man page Source code |
| normalization.sqrt | Man page Source code |
| normalization.trimmed.mean | Man page Source code |
| normalization.zscore | Man page |
| normalization.zscore.1 | Man page Source code |
| pa.distance.helper | Source code |
| pa.helper | Source code |
| pause | Source code |
| plotCellTypeEnrichment | Man page |
| plotHC | Man page |
| plotHeatmap | Man page |
| plotMarkers | Man page |
| plotPCASD | Man page |
| plotRDS | Man page |
| prefilterGenes | Man page |
| setAssociationTable | Source code |
| setCellMeta | Man page Source code |
| setCellNames | Man page Source code |
| setCellType | Man page Source code |
| setCellTypeEnrichment | Source code |
| setCellTypeMarkers | Man page Source code |
| setCellTypeValidation | Source code |
| setDF | Source code |
| setDiffGenes | Source code |
| setDiffTest | Source code |
| setES | Source code |
| setExpression | Man page Source code |
| setGeneMeta | Man page Source code |
| setGeneNames | Man page Source code |
| setGenesForClustering | Man page Source code |
| setHC | Source code |
| setPCA | Man page Source code |
| setSigGenes | Source code |
| setSigValidation | Source code |
| setTFs | Source code |
| setTSNE | Source code |
| signature.prediction | Man page |
| signature.prediction.1 | Man page Source code |
| signature.validation | Man page |
| sigpred.testing.sets | Man page Source code |
| sigpred.training.sets | Man page Source code |
| sincera | Man page |
| sincera-class | Man page |
| sincera_theme | Source code |
| specificity.criterion.selection | Man page Source code |
| specificity.helper | Source code |
| specificity.thresholdSelection | Man page Source code |
| triangle | Source code |
| trimmed.mean.helper | Source code |
| unique.helper | Source code |
| z.transform.helper | Source code |
