API for iaconogi/bigSCale2
A framework for the analysis of single cell data (RNA-seq and ATAC-seq) including clustering,phenotyping,pseudotime and inferring gene regulatory networks.
| Global functions | |
|---|---|
| C_compute_distances | Source code |
| DE_Rcpp | Source code |
| Pdistance | Source code |
| RecursiveClustering | Man page |
| ViewPseudo | Man page |
| batch.normalize | Source code |
| bigSCale | Man page |
| bigSCale-package | Man page |
| bigscale | Man page |
| bigscale.atac | Man page |
| bigscale.atac.pseudo | Man page |
| bigscale.classifier | Source code |
| bigscale.convert.h5 | Man page Source code |
| bigscale.generate.report | Man page Source code |
| bigscale.readMM | Man page Source code |
| bigscale.showLegend | Source code |
| bigscale.writeMM | Man page Source code |
| bigscaleDE | Man page |
| calculate.ODgenes | Source code |
| cap.expression | Source code |
| compare.centrality | Man page Source code |
| compute.atac.network | Man page |
| compute.distances.icell | Man page |
| compute.network | Man page |
| compute.network.model | Man page |
| computeMarkers | Man page |
| deconvolute | Man page Source code |
| distances_icells | Source code |
| enumerate | Source code |
| extract.cells | Man page Source code |
| fit.model | Source code |
| generate.edges | Source code |
| getClusters | Man page |
| getDistances | Man page |
| getMarkers | Man page |
| getSignatures | Man page |
| homogenize.networks | Man page Source code |
| homogenize.networks.internal | Source code |
| iCells | Man page |
| id.map | Source code |
| interactive.plot | Source code |
| jaccard_dist_text2vec_04 | Source code |
| mapAttributes | Source code |
| merge.chunks | Source code |
| mio_repvector_col | Source code |
| mio_repvector_row | Source code |
| nnz | Source code |
| pharse.10x.peaks | Source code |
| pick.sequences | Source code |
| preProcess | Man page |
| rcpp_hello_world | Man page Source code |
| remove.batches | Source code |
| restoreData | Man page |
| set.quantitative.palette | Source code |
| setClusters | Man page |
| setDCT | Man page |
| setDistances | Man page |
| setMarkers | Man page |
| setModel | Man page |
| setODgenes | Man page |
| shift.values | Source code |
| storeNormalized | Man page |
| storePseudo | Man page |
| storeTransformed | Man page |
| storeTsne | Man page |
| storeUMAP | Man page |
| sub.communities | Source code |
| substrRight | Source code |
| toCytoscape | Man page |
| transform.matrix | Source code |
| trim_sd | Source code |
| viewGeneBarPlot | Man page |
| viewGeneViolin | Man page |
| viewModel | Man page |
| viewODgenes | Man page |
| viewReduced | Man page |
| viewSignatures | Man page |
