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DOtools: A Toolkit for scRNA Data Analysis

DOtools.Rd

The `DOtools` package provides a set of functions for advanced data processing, visualisation, and statistical analysis in Seurat objects. It includes functions for cell-type prediction, reclustering, creating polished UMAP plots, subsetting Seurat objects, and various statistical analyses like Wilcoxon tests and SEM graphs.

Value

This is a package-level documentation file and does not return a value.

Details

This package includes the following functions:

  • DO.BoxPlot: A function for creating box plots with Wilcoxon test results.

  • DO.CellTypist: A function for running CellTypist on Seurat and SCE objects to predict cell types.

  • DO.DietSCE: A function for diet-based analysis of Seurat and SCE objects.

  • DO.Dotplot: A function for creating dot plots for visualizing gene expression.

  • DO.FullRecluster: A function for fine-grained reclustering of Seurat and SCE objects.

  • DO.BarplotClustert: A function for generating mean and SEM graphs for cluster-based analysis with t-tests.

  • DO.Barplot: A function for generating mean and SEM graphs with a statistical test indicating significance.

  • DO.Subset: A function for subsetting Seurat and SCE objects based on metadata.

  • DO.UMAP: A function for creating polished UMAP plots using either DimPlot or FeaturePlot.

  • DO.VlnPlot: A function for generating violin plots with Wilcoxon test results.

  • DO.CellComposition: A function for visualizing and statistically analyzing cell-type composition changes across conditions using the Scanpro Python package, with support for bootstrapping, proportion plots, and customizable output.

  • DO.Import: A function for building a merged Seurat and SCE object from 10x software output, or directly from provided tables.

  • DO.Integration: A function for integrating SCE objects and Seurat objects with the provided method.

  • DO.CellBender: A function for running CellBender in a virtual conda env with provided raw count h5 files.

  • DO.SplitBarGSEA: A function for viusalizing GSEA result from a provided df from e.g. metascape

  • DO.scVI: A function for running the scVI Integration implemented in scvi-tools.

  • DO.TransferLabel: A function for transfering annotation from a subseted object to the original seurat and SCE object.

  • DO.PyEnv: A function for creating a conda envrionment holding all python packages needed for some functions.

  • DO.Correlation: A function for creating a correlation plot between provided samples in the category specified.

  • DO.Heatmap: A function for generating Heat maps on gene expression data.

  • DO.HeatmapFC: A function for generating Heat maps showing foldchanges in expression between specified conditions.

  • DO.MultiDGE: A function for calculating DEGs on a single cell and speudo bulk level.

  • DO.EvalIntegration: A function for calculating sciB metrics on integration embeddings

  • dot-Do.BarcodeRanks: A function for estimating the number of expected cells and droplets.

  • dot-QC.Vlnplot: A function for estimating the number of expected cells and droplets.

  • dot-run_kbet: A self-contained call for running the kBET function.

  • dot-kBet_fct: A self-contained version of the kBET algorithm.

Author

Mariano Ruz Jurado, David Rodriguez Morales

See also

DO.BoxPlot, DO.CellTypist, DO.DietSCE, DO.Dotplot, DO.FullRecluster, DO.BarplotClustert, DO.Barplot, DO.Subset, DO.UMAP, DO.VlnPlot, DO.Import,DO.Integration, DO.CellBender, DO.SplitBarGSEA, DO.scVI, DO.TransferLabel,DO.Heatmap,DO.HeatmapFC, DO.PyEnv, DO.Correlation, DO.MultiDGE,DO.EvalIntegration, DO.TransferLabel, dot-Do.BarcodeRanks, dot-QC.Vlnplot, dot-run_kbet, dot-kBet_fct