Man pages for beyondpie/smmtools
Single-cell multi-omics sequenceing data tools
| ArchRPalettes | List of color palettes that can be used in plots |
| cleanOutfile | Create outdir if not exist, and remove the old file if... |
| eig_decomp | Get eigen decomposion Ref: SnapATAC eig_decomp |
| fastGetTSSEnrichmentSingleThread | Get TSS Enrichment scores |
| fastH5Read | Fast read H5 file Ref: ArchR .h5read |
| filterChrGR | filter ChrGR |
| getAnnotFromArchRData | get gene or genome Annotation from ArchR data. |
| getBlacklist | get black list |
| getBmatFromSnap | Get Bmat from Snap object. |
| getFragsOfAChrFromRawH5File | Get fragments from a given chromsome in rawH5File. Ref: ArchR... |
| getGeneMatrix | Generate Gene Matrix by directly mapping fragments onto... |
| getGmatFromSnap | Get Gmat from Snap object |
| getiFromSparseMatrix | Get i from sparseMatrix i index starts froms 1. Ref:... |
| getIndex | Get index in the subject vector for the query vector |
| getjFromSparseMatrix | Get j from sparseMatrix j index starts froms 1. Ref:... |
| getNfragmentPerBarcode | get numebr of fragments per barcode Ref: ArchR |
| getNormOVE | NormOVE from SnapATAC |
| getScrubletThresholdByMixEM | Another way to estimate the threshold for Scrublet Method... |
| getTileMatrix | Generate matrix of couts for each tile per cell |
| getTSSFromTxDb | get TSS from TxDb |
| getvalFromSparseMatrix | Get x/values from sparseMatrix |
| ggPoint | A ggplot-based dot plot wrapper function |
| installGenomeRelatedDatabase | Install genome/TxDb/OrgDb |
| loadBmatFromFile | Load SnapATAC Bmat from the h5 file generated by... |
| loadGeneMatrix | Load sparse matrix of gene matrix with both row and col names |
| loadSnapATACGmatFromFile | Load SnapATAC Gmat from the h5 file. |
| loadSparseMatrixFromMatTextFile | Load sparse matrix from mat file |
| loadTileMatrix | load TileMatrix into a sparseMatrix Ref: ArchR |
| paletteContinuous | Continuous Color Palette |
| paletteDiscrete | Optimized discrete color palette generation |
| plotDimReductElbow | Plot correlations between adjacent two principle components.... |
| plotDimReductPairwise | Plot correlations between adjacent two principle components.... |
| plot_scATAC_cnv | Generate Alleloscope object for analysis |
| readColumnsFromTextFile | Read file by columns |
| removeSampleName | Remove sampleName in barcodes if they have |
| runJaccard2 | Get Jaccard Matrix Ref: SnapATAC runJaccard2 |
| runKNN | Simplified runKNN in SnapATAC |
| runLeiden | Run Leiden algorithm as graph-based clustering. |
| runUMAP | Umap based on ArchR and Seuratdefault parameters |
| sampleBasedOnDepth | Sampling cells based on their sequencing depths without... |
| sampleBasedOnDepth2 | Sampling cells based on their sequencing depths without... |
| simplifyGRSeqnames | Remove chr in GRSeqnames |
| SnapATAC_BinarizeBmat | Binarize Bmat according SnapATAC |
| SnapATAC_DiffusionMaps | DiffusionMaps method in SnapATAC |
| SnapATACPalette | The color palettes from SnapATAC |
| SnapATAC_runDiffusionMaps | Core of DiffusionMaps for landmark cells. |
| SnapATAC_runDiffusionMapsExtension | Run DiffusionMaps for query cells baesd on the landmark... |
| SnapATAC_runHarmony | Perform batch effect using harmony |
| SnapATAC_runScrublet | Doublet removement using Scrublet |
| snapGmat2Seurat | Conver snap object to Seurat by gmat |
| subsetGeneAnnoByGenomeAnno | subset GeneAnnotation by GenomeAnnotation |
| subsetSeqnamesGR | get subset of GR |
| sumFragmentSingleThread | Transform original tabix File to H5File, then get... |
| suppressAll | Suppress message Ref: ArchR .suppressAll |
| tabixToH5SingleThread | Read fragment information |
| theme_ArchR | ggplot2 default theme for ArchR |
| tileChrom | tile ChromeSize Ref: ArchR |
| t.sparseMatrix | Transpose a sparseMatrix A method for the generics function... |
