API for r3fang/SnapATAC
Single Nucleus Analysis Package for ATAC-Seq
| Global functions | |
|---|---|
| .normOVE | Source code Source code |
| .valid.snap | Source code |
| .valid.snap.barcode | Source code |
| .valid.snap.feature | Source code |
| .valid.snap.peak | Source code |
| [,dim.reduct,ANY,ANY,ANY-method | Man page |
| [,jaccard,ANY,ANY,ANY-method | Man page |
| [,kgraph,ANY,ANY,ANY-method | Man page |
| [,snap,ANY,ANY,ANY-method | Man page |
| addBmatToSnap | Man page Source code |
| addBmatToSnap.default | Source code |
| addBmatToSnapSingle | Source code |
| addGmatToSnap | Man page Source code |
| addGmatToSnap.default | Source code |
| addGmatToSnapSingle | Source code |
| addPmatToSnap | Man page Source code |
| addPmatToSnap.default | Source code |
| addPmatToSnapSingle | Source code |
| barcodeInSnapFile | Man page Source code |
| barcodeInSnapFile.default | Source code |
| boxPlotFeature | Man page Source code |
| boxPlotFeature.default | Source code |
| calBmatCor | Man page Source code |
| calBmatCor.default | Source code |
| calJaccard | Source code |
| colMeans | Man page |
| colMeans,snap-method | Man page |
| colSums | Man page |
| colSums,snap-method | Man page |
| colVector | Source code |
| createColorPanel | Source code |
| createGmatFromMat | Man page Source code |
| createGmatFromMat.default | Source code |
| createPmat | Man page Source code |
| createSnap | Man page Source code |
| createSnap.default | Source code |
| createSnapFromBmat | Man page Source code |
| createSnapFromBmat.default | Source code |
| createSnapFromGmat | Man page Source code |
| createSnapFromGmat.default | Source code |
| createSnapFromPmat | Man page Source code |
| createSnapFromPmat.default | Source code |
| createSnapSingle | Source code |
| demo.sp | Man page |
| dim.reduct | Man page |
| dim.reduct-class | Man page |
| dimReductDim | Source code |
| eig_decomp | Source code |
| exportMetaData | Man page Source code |
| exportMetaData.default | Source code |
| extractReads | Man page Source code |
| extractReadsFromOneCell | Source code |
| fftRtsne | Source code |
| filterBins | Man page Source code |
| filterBins.default | Source code |
| filterCells | Man page Source code |
| filterCells.default | Source code |
| findCentrod | Source code |
| findDAR | Man page Source code |
| findDAR.default | Source code |
| findNegCells | Source code |
| getGraph | Source code |
| is.snap | Man page |
| is.snap,snap-method | Man page |
| isDimReductComplete | Source code |
| isKgraphEmpty | Source code |
| isSnapFile | Man page Source code |
| isSnapFile.default | Source code |
| jaccard-class | Man page |
| kgraph-class | Man page |
| makeBinary | Man page Source code |
| makeBinary.default | Source code |
| newSnap | Man page |
| normJaccard | Source code |
| normObservedJmat | Source code |
| normObservedJmat2 | Source code |
| nrow | Man page |
| nrow,snap-method | Man page |
| plotBarcode | Man page Source code |
| plotBarcode.default | Source code |
| plotBinCoverage | Man page Source code |
| plotBinCoverage.default | Source code |
| plotDimReductElbow | Man page Source code |
| plotDimReductElbow.default | Source code |
| plotDimReductPW | Man page Source code |
| plotDimReductPW.default | Source code |
| plotFeatureSingle | Man page Source code |
| plotFeatureSingle.default | Source code |
| plotGene | Man page Source code |
| plotGene.default | Source code |
| plotViz | Man page Source code |
| plotViz.default | Source code |
| predictGenePeakPair | Man page Source code |
| pvalue2fdr | Source code |
| readBins | Source code |
| readEdgeListFromFile | Source code |
| readMetaData | Man page Source code |
| readMetaData.default | Source code |
| readPeaks | Source code |
| rmBmatFromSnap | Man page Source code |
| rmBmatFromSnap.default | Source code |
| rmGmatFromSnap | Man page Source code |
| rmGmatFromSnap.default | Source code |
| rmPmatFromSnap | Man page Source code |
| rmPmatFromSnap.default | Source code |
| rowMeans | Man page |
| rowMeans,snap-method | Man page |
| rowSums | Man page |
| rowSums,snap-method | Man page |
| runChromVAR | Man page Source code |
| runCluster | Man page Source code |
| runCluster.default | Source code |
| runDiffusionMaps | Man page Source code |
| runDiffusionMapsExtension | Man page Source code |
| runDimReduct | Man page Source code |
| runDimReduct.default | Source code |
| runEigDecomp | Source code |
| runEigDecompExd | Source code |
| runHarmony | Man page Source code |
| runHarmony.default | Source code |
| runHomer | Man page Source code |
| runHomer.default | Source code |
| runJaccard | Man page Source code |
| runJaccard.default | Source code |
| runJaccard2 | Source code |
| runKNN | Man page Source code |
| runKNN.default | Source code |
| runLDA | Man page Source code |
| runLSA | Man page Source code |
| runMACS | Man page Source code |
| runMACSForAll | Man page Source code |
| runMagic | Man page Source code |
| runNormJaccard | Man page Source code |
| runNormJaccard.default | Source code |
| runSnapAddPmat | Man page Source code |
| runSnapAddPmat.default | Source code |
| runSnapAddPmatSingle | Source code |
| runViz | Man page Source code |
| runViz.default | Source code |
| scaleCountMatrix | Man page Source code |
| scaleCountMatrix.default | Source code |
| showBinSizes | Man page Source code |
| showBinSizes.default | Source code |
| snap-class | Man page |
| snapRbind | Man page Source code |
| snapToSeurat | Man page Source code |
| splitBmat | Source code |
| summarySnap | Man page |
| summarySnap,snap-method | Man page |
| textHalo | Source code |
| trainRegressModel | Source code |
| trainRegression | Source code |
| weightDimReduct | Source code |
| writeEdgeListToFile | Source code |
