tidyomics
This is the development version of tidyomics; for the stable release version, see tidyomics.
Easily install and load the tidyomics ecosystem
Bioconductor version: Development (3.24)
The tidyomics ecosystem is a set of packages for ’omic data analysis that work together in harmony; they share common data representations and API design, consistent with the tidyverse ecosystem. The tidyomics package is designed to make it easy to install and load core packages from the tidyomics ecosystem with a single command.
Author: Stefano Mangiola [aut, cre]
, Michael Love [aut]
, William Hutchison [aut]
Maintainer: Stefano Mangiola <mangiolastefano at gmail.com>
citation("tidyomics")):
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("tidyomics")
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("tidyomics")| Loading the tidyomics ecosystem | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.2) |
| Imports | tidySummarizedExperiment, tidySingleCellExperiment, tidySpatialExperiment, tidyseurat, plyranges, purrr, rlang, stringr, cli |
| System Requirements | |
| URL | https://github.com/tidyomics/tidyomics |
| Bug Reports | https://github.com/tidyomics/tidyomics/issues |
See More
| Suggests | utils, tidyr, dplyr, tibble, ggplot2, mockr (>= 0.2.0), knitr (>= 1.41), rmarkdown (>= 2.20), testthat (>= 3.1.6), nullranges, tidybulk, plyinteractions |
| 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 | tidyomics_1.9.0.tar.gz |
| Windows Binary (x86_64) | tidyomics_1.9.0.zip |
| macOS Binary (big-sur-x86_64) | tidyomics_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | tidyomics_1.9.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tidyomics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tidyomics |
| Bioc Package Browser | https://code.bioconductor.org/browse/tidyomics/ |
| Package Short Url | https://bioconductor.org/packages/tidyomics/ |
| Package Downloads Report | Download Stats |