Decontamination of single cell genomics data
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Documentation for package ‘decontX’ version 1.4.1
Help Pages
| decontX-package | The 'decontX' package. |
| .call_stan_vb | Call Stan variational bayes for inference |
| .process_stan_vb_out | Process Stan output. |
| decontPro | Decontaminate using decontPro |
| decontPro-method | Decontaminate using decontPro |
| decontX | Contamination estimation with decontX |
| decontX-method | Contamination estimation with decontX |
| decontXcounts | Get or set decontaminated counts matrix |
| decontXcounts-method | Get or set decontaminated counts matrix |
| decontXcounts<- | Get or set decontaminated counts matrix |
| decontXcounts<--method | Get or set decontaminated counts matrix |
| fastNormProp | Fast normalization for numeric matrix |
| fastNormPropLog | Fast normalization for numeric matrix |
| fastNormPropSqrt | Fast normalization for numeric matrix |
| nonzero | get row and column indices of none zero elements in the matrix |
| plotBoxByCluster | Boxplot of features grouped by cell type |
| plotDecontXContamination | Plots contamination on UMAP coordinates |
| plotDecontXMarkerExpression | Plots expression of marker genes before and after decontamination |
| plotDecontXMarkerPercentage | Plots percentage of cells cell types expressing markers |
| plotDensity | Density of each ADT, raw counts overlapped with decontaminated counts |
| retrieveFeatureIndex | Retrieve row index for a set of features |
| simulateContamination | Simulate contaminated count matrix |