Man pages for mathewchamberlain/veni
Generates QC plots, performs ambient RNA removal, and enhanced differential from single cell RNA sequencing data
| array_split | Split large data into smaller chunks |
| BatchProblemPlot | Inspect the shannon entropy of edges |
| CellBarPlot | Cells counts plot |
| CoverageBoxPlot | Plot a boxplot for genes detected |
| Decontaminate | Main function |
| DepthBoxPlot | Plot a boxplot for sequencing depth |
| DepthPlot | Plot genes detected vs. nUMI |
| DepthPlotComparison | Compare results before and after |
| FilterBackgroundMatrix | Filter background matrix |
| FilterBarcodes | Filter barcodes |
| FilterMito | Filter by Mito Fraction |
| GeneBoxPlot | Plot a boxplot for a single gene |
| GenerateLbls | Cells counts plot |
| GenerateSeuratObject | Convert a list of count matrices to a Seurat object |
| GetBackground | Get background distribution |
| GetBackgroundFromMatrix | Get background distribution |
| GetBackgroundMatrix | Get background matrix |
| GetCutoffs | Get suggested filter values |
| GetGeneFromNetwork | Load gene from network h5 file |
| GetMito | Get Mito Fraction |
| HClustBackgroundMatrix | Hierarchical cluster the background matrix |
| InspectBackground | Inspect background distribution |
| InspectBackgroundGenes | Inspect background genes in background matrix |
| InspectBackgroundMatrix | Inspect background matrix |
| JackD | Jackknife Differential Expression Analysis |
| LoadTxt | Load count matrix from a txt (or txt.gz) file |
| LoadTxtFolder | Load count matrix from a txt (or txt.gz) file |
| MitoBoxPlot | Plot a boxplot for the fraction of mitochondrial rna |
| QCPlots | Plot total genes and total counts histograms |
| Read10Xh5 | Load 10X count matrix from an h5 file |
| Read10Xh5Folder | Load 10X count matrix from an h5 file in each sub-folder |
| ReadCelseq | Load count matrix from a tsv (or tsv.gz) file |
| ReadDeconth5 | Load decont count matrix from an h5 file |
| ReadDeconth5Folder | Load decont count matrix from an h5 file in each sub-folder |
| ReadIndrop | Load Indrop count matrix from "matrix.txt" file |
| ReadIndropFolder | Load folder of Indrop count matrices from "matrix.txt" file |
| RegressMito | Regress MT percentage |
| SaveCountsToH5 | Write results to a folder |
| SaveNetworkH5 | Save network h5 files |
