Man pages for kharchenkolab/cacoa
Case-Control Analysis Tools for Single-Cell RNA-Seq
| addZScores | Add Z scores to DE results |
| appendStatisticsToDE | Append statistics to DE results |
| brewerPalette | Helper function for creating color palettes |
| Cacoa | Cacoa R6 class |
| checkData | Check cell count data |
| checkDataAndCells | Check data and list of cells |
| checkDataGroups | Check cell count data and groups |
| checkDataSbp | Check the agreement between sbp and cell count table |
| checkDataTree | Check agreement between Tree and the Cell count table |
| checkGroups | Check groups |
| checkSbp | Check sequential binary partitions(sbp) |
| checkSbpWhole | Check sequential binary partitions(sbp) for the whole set of... |
| checkTree | Check Tree |
| clusteredOntologyDotplot | Performs ontology clustering by genes and then shows medoids... |
| clusterGOsPerType | Cluster ontology terms per cell type |
| clusterIndividualGOs | Cluster individual ontology terms |
| clusterOntologyDF | Cluster Ontology DataFrame |
| collapseFamilies | Collapse ontology families |
| constructBestPartitionTree | Construct the canonical tree |
| constructTree | Construct the canonical tree |
| createDendrogram | helper function for creating dendograms |
| diffCellDensity | Estimate differential cell density |
| distanceBetweenTerms | Distance between terms |
| distTreeOrder | helper function for creating dendograms |
| enrichGOOpt | Enrich gene ontologies using enricher_internal |
| enrichGSEGOOpt | Estimate enriched GSEA terms using GSEA_internal |
| estimateCdaSpace | Internal function for estimating CDA space |
| estimateCellDensityGraph | Estimate graph smooth based cell density |
| estimateCellDensityKde | Estimate cell density in giving embedding, density will be... |
| estimateClusterPerGO | Estimate ontology clusters |
| estimateDEForTypeDESeq | estimate DE using DESeq2 |
| estimateDEForTypeEdgeR | Estimate DE using edgeR |
| estimateDEForTypeLimma | Estimate DE using limma |
| estimateDEForTypePairwiseStat | Estimate pair-wise DEGs |
| estimateDEPerCellTypeInner | Differential expression using different methods (DESeq2,... |
| estimateEnrichedGO | Estimate enriched GOs |
| estimateEnrichedGSEGO | Estimate enriched GSEA ontologies |
| estimateExpressionChange | Expression shift magnitudes per cluster between conditions |
| estimateGeneProgramsFabia | Estimate Gene Programs with FABIA |
| estimateOntologyClusterName | Estimate names for ontology clusters |
| estimateOntologyClusterNames | Estimate ontology cluster names |
| estimateOntologyFamilies | Estimate ontology families |
| estimateOntologyFromIds | Calculate ontologies based on DEs |
| extractCellGraph | Extract the cell groups from the object |
| extractCellGroups | Extract the cell groups from the object |
| extractEmbedding | Extract embeddings from the object |
| extractGeneExpression | Extract the gene expression from the object |
| extractJointCountMatrix | Extract the joint count matrix from the object |
| extractOdGenes | Extract the top overdispersed genes from the object |
| extractRawCountMatrices | Extract the cell groups from the object |
| extractSamplePerCell | Extract the sample/dataset per cell from the object |
| filterDEMetadata | Filter DE metadata |
| filterOntologies | Filter ontologies by adj. P |
| filterOntologyDf | Filter ontology dataframe |
| getDEEntrezIdsSplitted | Get DE ENTREZ IDs |
| getDensityContour | Extract contour from embedding |
| getExpressionFractionPerGroup | get expression fraction per cell group |
| getGenePalette | Get Gene Scale |
| getLoadings | Get loadings by different methods |
| getLogFreq | Get log frequencies from the cell count table |
| getNodeBalances | Get balances for all inner nodes of the tree |
| getOntologyFamilyChildren | Get ontology family children |
| getOntologyListLevels | Create list with ontology terms |
| getRndBalances | Get balances based on the random ilr basis |
| getRndPartition | Generate one random partition of given length |
| getRndSbp | Generate random sbp |
| groupOntologiesByCluster | Group ontologies by clusters |
| identifyFamilies | Identify ontology families |
| mapGeneIds | Map gene ENTREZ IDs to gene SYMBOLs |
| normalizePseudoBulkMatrix | Normalize pseudo-bulk matrix |
| plotCellLoadings | Internal plotting function for cell loadings |
| plotCellTypeSizeDep | Show a scatter plot of cell-type values vs. number of cells... |
| plotCodaSpaceInner | Internal plotting function to plot CoDA space |
| plotContrastTree | helper function for creating dendograms |
| plotCountBoxplotsPerType | Plot count boxplots per type |
| plotDensityKde | Plot cell density |
| plotHeatmap | Plot heatmap |
| plotMeanMedValuesPerCellType | Plot bar, point or boxplots showing mean/median values per... |
| plotNCellRegression | Plot number of cells regression |
| plotOntologyFamily | Plot related ontologies in one hierarchical network plot |
| prepareSamplesForDE | Prepare samples for DE analysis |
| produceResampling | This function produces the resampling dataset |
| rblapply | Iterate over tree (list of lists of lists, etc) for... |
| removeGroupEffect | Remove the strongest group effect from balances |
| sbp2tree | Get tree from balances |
| strpart | Split strings and extract nth element |
| subsetMatricesWithCommonGenes | Subset matrices with common genes |
| summarizeDEResamplingResults | Summarize DE Resampling Results |
| theme_legend_position | Helper function for creating color palettes Syncs input to... |
| validateDEPerCellTypeParams | Validate parameters per cell type |
| wrap_strings | Wrap strings for readibility on plots |
