Man pages for r3fang/SnapATAC
Single Nucleus Analysis Package for ATAC-Seq
| addBmatToSnap | Add cell-by-bin matrix |
| addGmatToSnap | Add cell-by-gene matrix |
| addPmatToSnap | Add cell-by-peak matrix |
| barcodeInSnapFile | Check barcode existance in snap file |
| boxPlotFeature | Feature Enrichment Boxplot |
| calBmatCor | Check correlation of cell-by-bin matrix |
| colMeans-methods | colMeans for snap objects |
| colSums-methods | colSums for snap objects |
| createGmatFromMat | Create Cell-by-Gene Matrix |
| createPmat | Create Cell-by-Peak Matrix |
| createSnap | Create a snap object from a snap file |
| createSnapFromBmat | Create a snap object from cell-by-bin matrix |
| createSnapFromGmat | Create a snap object from cell-by-gene matrix |
| createSnapFromPmat | Create a snap object from cell-by-peak matrix |
| demo.sp | Single Nucleus ATAC-seq Object |
| dim.reduct-class | An S4 class to represent dimentionality reduction object. |
| exportMetaData | Export barcode meta data |
| extractReads | Extract Reads By Barcodes |
| filterBins | Feature filtration |
| filterCells | Cell filtration |
| findDAR | Identifiy Differential Accessible Regions (DARs) |
| isSnapFile | Check a snap-format file |
| is.snap-methods | Check snap object |
| jaccard-class | An S4 class jaccard to represent a jaccard object. |
| kgraph-class | An S4 class jaccard to represent a knn graph object. |
| makeBinary | Convert the count matrix to binary matrix |
| newSnap | Create an empty snap object |
| nrow-methods | nrow for snap object. |
| plotBarcode | Plot Barocde Quality Control Distribution |
| plotBinCoverage | Plot Bin Coverage Distribution |
| plotDimReductElbow | Elbow Plot for Dimentionality Reduction Result |
| plotDimReductPW | Pairwise plot for Dimentionality Reduction Result |
| plotFeatureSingle | plotFeatureSingle |
| plotGene | Plot gene-body accessibility level |
| plotViz | Visulization |
| predictGenePeakPair | Link Distal Regulatory Elements (peaks) to Putative Target... |
| readMetaData | Read meta data from a snap file |
| rmBmatFromSnap | Remove cell-by-bin matrix |
| rmGmatFromSnap | Remove cell-by-gene matrix |
| rmPmatFromSnap | Remove cell-by-peak matrix |
| rowMeans-methods | rowMeans for snap objects |
| rowSums-methods | rowSums for snap objects |
| runChromVAR | Estimate Motif Variability Using ChromVAR |
| runCluster | Find Clusters Using Louvain/Leiden Algorithm |
| runDiffusionMaps | Dimentionality Reduction by Diffusion Maps Algorithm |
| runDiffusionMapsExtension | Diffusion Maps Extension |
| runDimReduct | Linear Dimentionality Reduction |
| runHarmony | Perform batch effect using harmony |
| runHomer | Motif Analysis Using Homer |
| runJaccard | Calcualte Jaccard Index Matrix |
| runKNN | K Nearest Neighbour Graph Construction |
| runLDA | Latent Dirichlet Allocation |
| runLSA | Latent Semantic Analysis |
| runMACS | Call Peaks Using MACS2 |
| runMACSForAll | Call Peaks Using MACS2 For All Clusters |
| runMagic | Affinity Graph-based Smoothing |
| runNormJaccard | Normalize Jaccard Index Matrix |
| runSnapAddPmat | Add cell-by-peak matrix to a snap file |
| runViz | Dimentionality Reduction for Visualization |
| scaleCountMatrix | Normlaize Count Matrix |
| showBinSizes | Show bin sizes in a snap file |
| snap-class | An S4 class snap to represent single-nucleus accessibility... |
| snapRbind | Combine snap objects |
| snapToSeurat | Convert a snap object to a seurat object |
| sub-dim.reduct-ANY-ANY-ANY-method | subsetting for dim.reduct objects |
| sub-jaccard-ANY-ANY-ANY-method | subsetting for jaccard objects |
| sub-kgraph-ANY-ANY-ANY-method | subsetting for kgraph objects |
| sub-snap-ANY-ANY-ANY-method | subsetting for snap objects |
| summarySnap-methods | summarySnap for snap object. |
