Man pages for dkeitley/scrabbitr
Single-cell RNA-seq analysis of rabbit gastrulation
| calcGeneSpec | Calculates gene specificity values |
| calcNhoodMean | Average expression values within each neighbourhood |
| calcNhoodSim | Compare neighbourhoods across species |
| downsampleSCE | Uniformly downsample a SingleCellExperiment object |
| exportToGMT | Write colData to a GMT file |
| filterSharedFeatures | Obtain one-to-one orthologs from Ensembl. |
| getEnsemblHomologs | Queries Ensembl BioMart database for homologs between... |
| getGenesFromGOTerms | Used to obtain genes related to apoptosis and proliferation... |
| getSharedUniqueMarkers | Get dataframe of shared and unique markers. Used for... |
| isEnsemblID | Checks if provided genes are in Ensembl gene ID format.... |
| loadReadsAroundGRange | Obtains reads within a window of a given GRange |
| loadTyser2020 | Load human data from Tyser et al. 2021 |
| loadWOTData | Load csv files exported from WOT trajectory/fate AnnData |
| loadYang2021 | Load macaque data from Yang et al. 2021 |
| plotAnnotatedUMAP | Plot a UMAP with annotated labels Used to show predicted cell... |
| plotNhoodSimGroups | sim_values in order of milo nhoods TODO: Make into separate... |
| plotReadDistsNearGene | Plots histogram of distances of reads that are nearest to the... |
| prepareEdgeR | Prepare groupings in SingleCellExperiment object for running... |
| runEdgeR | Compute differentially expressing genes using EdgeR |
