tidybulk
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see tidybulk.
Brings transcriptomics to the tidyverse
Bioconductor version: 3.13
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")):
Installation
To install this package, start R (version "4.1") 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")| Comparison with base R | HTML | R Script |
| Manuscript code - differential feature abundance | HTML | R Script |
| Manuscript code - transcriptional signature identification | 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 | 1.4.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | GPL-3 |
| Depends | R (>= 4.1.0) |
| Imports | tibble, readr, dplyr, magrittr, tidyr, stringr, rlang, purrr, preprocessCore, stats, parallel, utils, lifecycle, scales, SummarizedExperiment, methods |
| System Requirements | |
| URL |
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, S4Vectors, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional, survminer, tidySummarizedExperiment, markdown |
| 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 | tidybulk_1.4.0.tar.gz |
| Windows Binary | tidybulk_1.4.0.zip |
| macOS 10.13 (High Sierra) | tidybulk_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tidybulk |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tidybulk |
| Bioc Package Browser | https://code.bioconductor.org/browse/tidybulk/ |
| Package Short Url | https://bioconductor.org/packages/tidybulk/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |