Man pages for YY-SONG0718/scfindME
This is a package that adaps "scfind", a search tool for single cell RNA-seq data by gene lists, to alternative splicing analysis
| addIndexMeta | Add necessary elements of the metadata slot of an... |
| buildAltSpliceIndex | Builds an 'SCFind' object from a 'matrix' |
| cellTypeMarkers | return all the gene markers for a specified cell.type |
| cellTypeNames | Return a vector with all existing cell type names in the... |
| evaluateMarkers | Evaluate a user specific query by calculating the precision... |
| findCellTypes | queries cells that contain all the genes from the list |
| findCellTypeSpecificities | Find out how many cell-types each gene is found |
| findHouseKeepingNodes | Find the set of genes that are ubiquitously expressed in a... |
| findNodeSets | This function finds coordinated node sets for a gene |
| findNodeSignatures | Find the signature genes for a cell-type |
| findSimilarNodes | Look at all other genes and rank them based on the similarity... |
| findTissueSpecificities | Find out how many tissues each gene is found |
| geneNodes | This function retrieves node details in an index by gene id... |
| get.cell.type.raw.psi | This function gets the raw PSI of a node in a cell type |
| getCoordinatedNodes | This function finds coordinated node sets for a gene |
| get_lower_tri | Get lower triangle of the correlation matrix |
| getRawPsi | This function gets the raw PSI of a node in a cell type |
| get_upper_tri | # Get upper triangle of the correlation matrix |
| hyperQueryCellTypes | Runs a query and performs the hypergeometric test for the... |
| loadObject | Generic to be used instead of readRDS |
| markerNodes | Performs query optimization and return the best candidate... |
| mergeDataset | Merges an external index into the existing object |
| mergeIndices | merge two elias fano indices |
| nodeDetails | This function retrieves node details by node id |
| plotRawPsiCorr | This function plots correlation of splicing PSI and return... |
| plotRawPsiHeatmap | This function plots heatmap of PSI values |
| reorder_cormat | reorder correlation matrix |
| saveObject | Generic to be used instead of saveRDS |
| SCFind-class | The scfind main class object |
| scfindNodes | Get all nodes in the database |
| Tasic_2016 | Example SCFind alternative splicing index 'Tasic_2016'... |
