Man pages for plantformatics/Socrates
Analysis of scATAC-seq data
| buildMetaData_OG | buildMetaData_OG |
| callACRs | callACRs |
| callClusters | Cluster cells using Louvain, Leiden or other graph-based... |
| cleanData | Filter sparse matrix |
| coAccess | coAccess |
| convertSparseData | convertSparseData |
| countRemoveOrganelle | countRemoveOrganelle |
| detectDoublets | detectDoublets |
| filtDistClst | Filter singleton cells from the UMAP embedding by distance... |
| filterDoublets | filterDoublets |
| filterSingle | Filter singleton cells from the UMAP embedding |
| findCells_OG | findCells |
| generateMatrix | generateMatrix |
| getFDR | getFDR |
| isCell | isCell |
| loadBEDandGenomeData | loadBEDandGenomeData |
| loadSparseData | loadSparseData |
| logisticModel | Accessibility residuals from unconstrained quasibinomial... |
| mergeQCdataRDS | mergeQCdataRDS |
| mergeSocratesRDS | mergeSocratesRDS |
| plotUMAP | Plot UMAP embeddings |
| projectUMAP | Project cells into a reduced embedding with UMAP |
| reduceDims | Reduce dimensions of residual matrix |
| regModel | Regularized quasibinomial logistic regression |
| regModel2 | Regularized quasibinomial logistic regression |
| runCicero | runCicero |
| standardizeResiduals | standardize or center residuals |
| tfidf | TF-IDF normalization |
| writeReadME | writeReadME |
