DOtools
This is the released version of DOtools; for the devel version, see DOtools.
Convenient functions to streamline your single cell data analysis workflow
Bioconductor version: Release (3.22)
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]
, David Rodriguez Morales [aut]
, David John [aut]
, DFG SFB 1366, Project B04 [fnd], DFG SFB 1531, Project 456687919 [fnd]
Maintainer: Mariano Ruz Jurado <ruzjurado at med.uni-frankfurt.de>
citation("DOtools")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, Clustering, GeneExpression, QualityControl, RNASeq, SingleCell, Software, Visualization, WorkflowStep |
| Version | 1.0.0 |
| 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 |
See More
| Suggests | SummarizedExperiment, knitr, kableExtra, pkgdown, RefManageR, BiocStyle, roxygen2, httr, magick, rmarkdown, assertthat, plyr, rsvg, scran, scater, igraph, sessioninfo, testthat (>= 3.0.0), mockery |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DOtools_1.0.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/DOtools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DOtools |
| Bioc Package Browser | https://code.bioconductor.org/browse/DOtools/ |
| Package Short Url | https://bioconductor.org/packages/DOtools/ |
| Package Downloads Report | Download Stats |