Man pages for nbroguiere/burgertools
Collection of tools extending the functionality of Seurat
| AnnotatedVariableFeaturePlot | Annotated variable features plot |
| AnnotateWithTCGA | Annotate with TCGA |
| AnnotateWithVEP | Annotate variants with VEP data. |
| CellSimilarityToGenotypes | Compute the similarity of single cells in a Seurat object to... |
| Classify | Automatic cell type classification based on signatures |
| ClassifyManual | Manual cell type classification by applying gates |
| ComputeMitoContent | Compute the fraction/percentage of mitochondrial genes (mouse... |
| CreateGenotypeObject | Create a genotype object |
| CrossImpute | MAGIC imputation of features of an assay based on the... |
| Export10X | Reexport the data from a Seurat object in 10X format |
| ExportGenotype | Reexport vartrix matrices from a genotype object |
| FindDifferentVariants | Find differentially frequent variants between two populations |
| FindInformativeVariants | Find informative variants |
| FractionDifferingVariants | Fraction of differing variants |
| GatherFeatures | Gather features |
| GenerateGates | Generate gates based on pair of thresholds (minimum main... |
| genotype-class | Object storing genotypes and variant metadata |
| GenotypeSimilarityHeatmap | Genotype similarity heatmap |
| GetAllSignatureGenes | Get all signature genes |
| IdentPlotQC | QC plot with cell type highlight |
| Import10X | Import data in the 10X format with eventual metadata and... |
| Impute | MAGIC imputation |
| InformativeVariantPlot | Plot the informative variants with annotations |
| NormalizeHTO | Normalize hashtag oligo data |
| PrefilterVartrix | Prefilter variants by coverage in the vartrix matrices |
| PseudoBulkGenotypes | Aggregate pseudo-bulk genotypes |
| ReadSignatures | Read signatures in .gmt format |
| ReadTCGA | Load TCGA data |
| ReadVartrix | Load vartrix data |
| ReadVcf | Read a vcf file |
| ReadVEP | Read a VEP tsv file |
| RunMDS | Run MDS |
| RunQC | QC by cell type |
| ScoreSignature | Signature scoring on Seurat objects |
| ScoreSignatures | Multiple signature scoring on Seurat objects |
| SeuratAddVariants | Add the variant information contained in a genotype object to... |
| SignaturePlotQC | QC plot with signatures highlight |
| SignatureScatterPlot | Scatter plots of signature scores on single cells |
| TagCells | Quickly tag cells in a Seurat Object |
| VariantPlot | Plots variants |
| WriteSignatures | Write signatures in .gmt format |
