Man pages for linquynus/RCAv2-beta
Reference Component Analysis
| buildReferencePanel | Function to build a reference panel from your bulk RNA... |
| ComputePairWiseDE | Find markers (differentially expressed genes) between two... |
| computeUMAP | Compute a umap projection into 2 or 3 dimensions |
| createRCAObject | Create RCA object |
| createRCAObjectFrom10X | Create RCA Object from 10X data |
| dataClust | Generate cell clusters using hierarchical clustering and... |
| dataDE | Compute pairwise DE genes for supervised clustering result. |
| dataFilter | Filter the dataset and remove genes and cells that could be... |
| dataLogNormalise | Log-transform and normalise data by sequencing depth |
| dataProject | Compute Reference Component features for clustering analysis |
| dataSClust | Generate cell clusters using Seurat graph based clustering. |
| dataSNN | Generate cell clusters using hierarchical clustering and... |
| doEnrichGo | Perform GO enrichment analysis using cluster profiler. |
| doEnrichKEGG | Perform KEGG enrichment analysis using cluster profiler. |
| estimateCellTypeFromProjection | Estimate the most likely cell type from the projection to the... |
| estimateCellTypeFromProjectionPerCluster | Estimate the most likely cell type from the projection to the... |
| parameterSpaceSeurat | Generates a data frame showcasing the dependence between... |
| parameterSpaceSNN | Generates an overview on the dependence of SNN parameters to... |
| performClusterSpecificQC | Filter the dataset and remove genes and cells that could be... |
| plotClusterQuality | Perform cluster specific QC |
| plotDEHeatmap | Plot heatmap of DE genes |
| plotRCAClusterComposition | Plot bar plots showing the composition of RCA clusters |
| plotRCAHeatmap | Plot heatmap of projection to the RCA panel |
| plotRCAUMAP | Plot umap of projection to the RCA panel |
| plotRCAUMAP3D | Plot umap of projection to the RCA panel |
| RCA-class | RCA Class |
| VioplotQCForCluster | Fviolin plot of QC metrics |
