Man pages 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.
| bigscale | bigSCale2.0 |
| bigscale.atac | bigSCale ATAC |
| bigscale.atac.pseudo | bigSCale ATAC Pseudo (IN DEVELOPMENT, DO NOT USE) |
| bigscale.convert.h5 | bigscale.convert.h5 |
| bigscaleDE | Differential Expression |
| bigscale.generate.report | bigscale.generate.report |
| bigSCale-package | A short title line describing what the package does |
| bigscale.readMM | bigscale.readMM |
| bigscale.writeMM | bigscale.writeMM |
| compare.centrality | Compare gene centralities |
| compute.atac.network | ATAC-seq Gene regulatory network |
| compute.distances.icell | Compute iCell distances |
| computeMarkers | computeMarkers |
| compute.network | Gene regulatory network |
| compute.network.model | Compute network model |
| deconvolute | deconvolute |
| extract.cells | extract.cells |
| getClusters | getClusters |
| getDistances | getDistances |
| getMarkers | getMarkers |
| getSignatures | getSignatures |
| homogenize.networks | homogenize.networks |
| iCells | iCells |
| preProcess | preProcess |
| rcpp_hello_world | Simple function using Rcpp |
| RecursiveClustering | RecursiveClustering |
| restoreData | restoreData |
| setClusters | setClusters |
| setDCT | setDCT |
| setDistances | setDistances |
| setMarkers | setMarkers |
| setModel | setModel |
| setODgenes | setODgenes |
| storeNormalized | storeNormalized |
| storePseudo | storePseudo |
| storeTransformed | storeTransformed |
| storeTsne | storeTsne |
| storeUMAP | storeUMAP |
| toCytoscape | bigscale.toCytoscape |
| viewGeneBarPlot | viewGeneBarPlot |
| viewGeneViolin | viewGeneViolin |
| viewModel | viewModel |
| viewODgenes | viewODgenes |
| ViewPseudo | ViewPseudo |
| viewReduced | viewReduced |
| viewSignatures | atures |
