tidybulk
This is the released version of tidybulk; for the devel version, see tidybulk.
Brings transcriptomics to the tidyverse
Bioconductor version: Release (3.23)
This is a collection of utility functions that allow to perform exploration of and calculations to RNA sequencing data, in a modular, pipe-friendly and tidy fashion.
Author: Stefano Mangiola [aut, cre], Maria Doyle [ctb]
Maintainer: Stefano Mangiola <mangiolastefano at gmail.com>
citation("tidybulk")):Stefano Mangiola. tidybulk: Brings transcriptomics to the tidyverse. doi:10.18129/B9.bioc.tidybulk, R package version 2.2.0, https://bioconductor.org/packages/tidybulk.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tidybulk")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("tidybulk")| Side-by-side comparison with standard interfaces | HTML | R Script |
| Overview of the tidybulk package | HTML | R Script |
| Reference Manual |
Details
| biocViews | AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics |
| Version | 2.2.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.4.0), ttservice (>= 0.3.6) |
| Imports | tibble, dplyr (>= 1.1.0), magrittr, tidyr, stringr, rlang, purrr, tidyselect, stats, parallel, utils, lifecycle, scales, ggplot2, SummarizedExperiment, GenomicRanges, methods, S4Vectors, crayon, Matrix |
| System Requirements | |
| URL | https://github.com/stemangiola/tidybulk |
| Bug Reports | https://github.com/stemangiola/tidybulk/issues |
See More
| Suggests | BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, fastmatch, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, preprocessCore, igraph, EGSEA, IRanges, here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS, pkgconfig, enrichplot, patchwork, airway |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | tidyexposomics |
| Suggests Me | tidyomics |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tidybulk_2.2.0.tar.gz |
| Windows Binary (x86_64) | tidybulk_2.2.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | tidybulk_2.2.0.tgz |
| macOS Binary (sonoma-arm64) | tidybulk_2.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tidybulk |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tidybulk |
| Package Short Url | https://bioconductor.org/packages/tidybulk/ |
| Package Downloads Report | Download Stats |