DOtools

This is the development version of DOtools; for the stable release version, see DOtools.

Convenient functions to streamline your single cell data analysis workflow

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.DOtools

Bioconductor version: Development (3.23)

This package provides functions for creating various visualizations, convenient wrappers, and quality-of-life utilities for single cell experiment objects. It offers a streamlined approach to visualize results and integrates different tools for easy use.

Author: Mariano Ruz Jurado [aut, cre] ORCID iD ORCID: 0000-0001-5354-5336 , David Rodriguez Morales [aut] ORCID iD ORCID: 0000-0002-1819-6991 , David John [aut] ORCID iD ORCID: 0000-0003-3217-5449 , DFG SFB 1366, Project B04 [fnd], DFG SFB 1531, Project 456687919 [fnd]

Maintainer: Mariano Ruz Jurado <ruzjurado at med.uni-frankfurt.de>

Citation (from within R, enter citation("DOtools")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("DOtools")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DOtools")

Quality control of sc/snRNA-seq HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, Clustering, GeneExpression, QualityControl, RNASeq, SingleCell, Software, Visualization, WorkflowStep

Version 1.1.0

In Bioconductor since BioC 3.22 (R-4.5) (< 6 months)

License MIT + file LICENSE

Depends R (>= 4.5.0)

Imports Seurat (>= 5.2.0), SeuratObject (>= 5.1.0), ggplot2 (>= 3.5.0), ggpubr (>= 0.6.0), ggtext (>= 0.1.2), ggalluvial (>= 0.12.5), tidyverse (>= 2.0.0), reshape2 (>= 1.4.4), dplyr (>= 1.1.4), tidyr (>= 1.3.1), rstatix (>= 0.7.2), cowplot (>= 1.1.3), reticulate (>= 1.41.0.1), zellkonverter(>= 1.16.0), progress (>= 1.2.3), ggiraphExtra (>= 0.3.0), grid (>= 4.4.3), SCpubr (>= 2.0.2), DropletUtils(>= 1.26.0), scCustomize (>= 3.0.1), openxlsx (>= 4.2.8), tibble (>= 3.2.1), scDblFinder(>= 1.20.0), ggcorrplot (>= 0.1.4.1), DESeq2(>= 1.48.1), enrichR (>= 3.4), cli (>= 3.6.5), curl (>= 6.3.0), magrittr (>= 2.0.3), Matrix (>= 1.7.3), purrr (>= 1.0.4), rlang (>= 1.1.6), scales (>= 1.4.0), SingleCellExperiment(>= 1.30.1), S4Vectors(>= 0.46.0), basilisk(>= 1.20.0), methods, stats, utils

System Requirements

URL https://marianoruzjurado.github.io/DOtools/

Bug Reports https://github.com/MarianoRuzJurado/DOtools/issues