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
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, Clustering, GeneExpression, QualityControl, RNASeq, SingleCell, Software, Visualization, WorkflowStep |
| Version | 1.3.5 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| 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), ggrastr (>= 1.0.2), 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), glmGamPoi(>= 1.24.0), 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), FNN (>= 1.1.4.1), ks, 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), leidenbase (>= 0.1.36), 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_1.3.5.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | DOtools_1.3.5.tgz |
| macOS Binary (sonoma-arm64) | DOtools_1.3.5.tgz |
| 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 |