Man pages for hemberg-lab/scfind
A search tool for single cell RNA-seq data by gene lists
| buildCellTypeIndex | Builds an 'SCFind' object from a 'SingleCellExperiment'... |
| 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... |
| ExampleIndex | Single cell RNA-Seq datasets extracted from a publication by... |
| findCellTypes | queries cells that contain all the genes from the list |
| findCellTypeSpecificities | Find out how many cell-types each gene is found |
| findGeneSignatures | Find the signature genes for a cell-type |
| findHouseKeepingGenes | Find the set of genes that are ubiquitously expressed in a... |
| findSimilarGenes | Look at all other genes and rank them based on the similarity... |
| findTissueSpecificities | Find out how many tissues each gene is found |
| hyperQueryCellTypes | Runs a query and performs the hypergeometric test for the... |
| loadObject | Generic to be used instead of readRDS |
| markerGenes | Performs query optimization and return the best candidate... |
| mergeDataset | Merges an external index into the existing object |
| mergeIndices | merge two elias fano indices |
| mergeSCE | Merges a SingleCellExperiment object into the SCFind index |
| saveObject | Generic to be used instead of saveRDS |
| scfind | Minimal Rcpp Module Example |
| SCFind-class | The scfind main class object |
| scfindGenes | Get all genes in the database |
| scfindShiny | Opens 'scfind' index in an interactive session in a web... |
| scfindShinyServer | Server handler for scfind |
| tm10x | Single cell RNA-Seq data extracted from a publication by the... |
| tmfacs | Single cell RNA-Seq data extracted from a publication by the... |
| ui.scfind | UI handler for the shiny front end of scfind |
