Man pages for connorhknight/IBRAP
Integrated Benchmarking scRNA-seq Analytical Pipeline (IBRAP)
| add.cell.cycle | Scores cell cycle phases |
| add.feature.score | Provides scores for a given vector of features |
| as.csc.matrix | converts to sparse matrix |
| as_list_methods | Method override for as.list function regarding methods S4... |
| as_matrix | converts to matrix |
| as_matrix_transpose | converts to transposed matrix |
| benchmark.clustering | Benchmarks the cluster assignments |
| benchmark.integration | Benchmarks the cluster assignmentws |
| cell_metadata | Generates cell-level metadata |
| createIBRAPobject | Create an IBRAP class object |
| df_to_dgCMatrix | converts to dgCMatrix |
| dim | Method override for dim function |
| dollar | Method override for ”$” subset function regarding IBRAP S4... |
| feature_metadata | Generates feature level metadata |
| filter_IBRAP | Filters object according to cell metadata |
| find_percentage_genes | Calculates the fraction of counts from genes matching a... |
| IBRAP-object | S4 class object that contains method-assays |
| integrate.cluster.benchmarking.results | Integrates all cluster benchmarking into a single dataframe |
| isUnique | Are vector items unique |
| merge | Method override for merge function regarding IBRAP S4 objects |
| methods-object | An S4 class object of method-assays |
| ncol | Method override for ncol function |
| nrow | Method override for nrow function |
| perform.bbknn | Performs BBKNN integration |
| perform.celltalker | Infers cell-to-cell communications. |
| perform.decontX | R package: celda, decontX function |
| perform.diffexp | Perform differential expression |
| perform.diffexp.all | Perform differential expression one cluster vs all |
| perform.diffusion.map | Diffusion maps |
| perform.GO.enrichment | Gene Ontology enrichment |
| perform.graph.cluster | Performs graph-based clustering |
| perform.graph.subclustering | Seurat subclustering |
| perform.gsea | Returnas gene set enrichment scores for indivdiual cells |
| perform.harmony | Performs Harmony integration |
| perform.lvish | Performs LargeVis reduction |
| perform.nn | Finds the shared nearest neighbourhood for the cells. This... |
| perform.pca | Performs PCA reduction |
| perform.reduction.kmeans | Performs Kmeans/PAM clustering on a reduction |
| perform.sc3.reduction.cluster | Performs SC3 clustering on reduced embeddings |
| perform.sc3.slot.cluster | Performs SC3 clustering on matrix slot |
| perform.scanorama | Performs Scanorama integration |
| perform.scanpy | Performs Scanpy normalisation, hvg selection, scaling and... |
| perform.scran | Performs Scran normalisation, hvg selection, scaling and... |
| perform.scrublet | Python module: scrublet |
| perform.sct | Performs SCTransform |
| perform.sctype | Performs sctype |
| perform.seurat.cca | Performs Seurat Integration |
| perform.singleR.annotation | Performs automated cell annotation on query datasets using... |
| perform.slingshot.trajectory | Performs Slingshot trajectory inference |
| perform.tpm | Performs TPM normalisation |
| perform.tsne | Performs t-SNE reduction |
| perform.umap | Performs UMAP reduction |
| plot.dot.plot | Plots a dot plot of gene expression |
| plot.features | Plot of reduced dimensions and features |
| plot.GO.output | Plot GO enrichment output |
| plot.QC.scatter | Plots two QC metrices in scatter format |
| plot.QC.vln | Plots a given QC metric |
| plot.reduced.dim | Plot of reduced dimensions and labels |
| plot.reduced.dim.interactive | Interactive plot of reduced dimensions and labels |
| plot.slingshot | Plots slingshot results |
| plot.variance | Plot reduction explained variance |
| plot.vln | Plot of violin plot of defined features |
| prepare.for.dittoSeq | Create a SCE object to use for creating plots in dittoSeq |
| prepare.reticulate | Installs or identifies if python modules are installed |
| Read10X_output | Produce counts matrix from CellRanger output |
| remove.hvgs | Remove highly variable genes |
| replaceResults | Shows the contents in your IBRAP object |
| rownames | Method override for rownames function |
| run.IBRAP.rshiny | Rshiny application initiator |
| showObjectContents | Shows the contents in your IBRAP object |
| splitIBRAP | Split the IBRAP object up |
| sub-IBRAP-ANY-ANY-ANY-method | Method override for ”[” subset function regarding IBRAP S4... |
