Man pages for yavorska/TenXAnalysisPackage
Analysis of the 10x Genomics 1.3 Million Cells Data
| cellCounts | Return cellCounts data.frame |
| cellCountsExpr | Return the total number of genes expressed for each cell |
| cellCountsTrans | Return the total number of transcripts for each cell |
| cellGroup | Return the cellGroup vector |
| cellIndex | Cells in data |
| cellLib | Return the libraryID vector |
| cellMouse | Return the mouseID vector |
| cellN | Total number of cells in the data set |
| determineGeneFromGO | Find genes associated with a GO term |
| determineGeneFromQuery | Find genes containing some query in their GO description |
| determineGeneID | Find gene name in data |
| determineGOFromGene | Find GO terms associated with a gene |
| determineGroupAnnotations | Determine group annotations |
| determineLibraryAnnotations | Determine library annotations |
| determineLibraryFromGroup | Get the library that this group belongs to |
| determineMouseFromGroup | Get the mouse that this group belongs to |
| determineSampleFromGroup | Get indices of cells in a group |
| EG2GO | GO annotation data file |
| geneCounts | Return geneCounts data.frame |
| geneENSEMBL | Return the ENSEMBL names of the genes |
| geneExpressed | Return geneExpressed data.frame |
| geneIndex | Genes in data |
| geneN | Total number of genes in the data set |
| geneNames | Return the HGNC names of the genes |
| generateSubset | Generate a TenXSubset object |
| generateSummaryExpr | Generate a summary counts object |
| groupN | Total number of groups in the data set |
| groupSize | Size of summary groups |
| libN | Total number of libraries in the data set |
| plotTenX | TenXSubset object data summaries |
| plotTenXGene | Plot gene summary for TenXSubset object |
| plotTenXGeneCor | Compare gene expression across multiple genes |
| plotTenXGeneGO | Plot GO summary for specified gene set |
| plotTenXGenePair | Compare gene expression profiles for two genes |
| plotTenXGO | Plot GO summary for TenXSubset object |
| plotTenXGroupExpr | Plot how gene expression changes based on library |
| plotTenXMouseExpr | Plot how gene expression changes based on mouse |
| TenXse_colData | colData of the original data set |
| TenXse_rowData | rowData of the original data set |
| TenXSubsetAll | Summary file for entire data set |
| TenXSubset-class | Class used to represent the grouped TenXData. The object... |
