tidybulk

DOI: 10.18129/B9.bioc.tidybulk    

This is the development version of tidybulk; for the stable release version, see tidybulk.

Brings transcriptomics to the tidyverse

Bioconductor version: Development (3.17)

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>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

HTML	R Script	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
PDF		Reference Manual

Details

biocViews	AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version	1.11.0
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 years)
License	GPL-3
Depends	R (>= 4.1.0)
Imports	tibble, readr, dplyr, magrittr, tidyr, stringi, stringr, rlang, purrr, tidyselect, preprocessCore, stats, parallel, utils, lifecycle, scales, SummarizedExperiment, GenomicRanges, methods, S4Vectors, crayon
LinkingTo
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, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, igraph, EGSEA
SystemRequirements
Enhances
URL	https://github.com/stemangiola/tidybulk
BugReports	https://github.com/stemangiola/tidybulk/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	tidybulk_1.11.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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