tidybulk

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see tidybulk.

Brings transcriptomics to the tidyverse

Bioconductor version: 3.12

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 (from within R, enter citation("tidybulk")):

Installation

To install this package, start R (version "4.0") 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 transcript abundance HTML R Script

Manuscript code - transcriptional signature identification HTML R Script

Overview of the tidybulk package HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics

Version 1.2.1

In Bioconductor since BioC 3.11 (R-4.0) (4 years)

License GPL-3

Depends R (>= 4.0.0)

Imports tibble, readr, dplyr, magrittr, tidyr, stringr, rlang, purrr, preprocessCore, stats, parallel, utils, lifecycle, scales, SummarizedExperiment, methods

System Requirements

URL

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

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_1.2.1.tar.gz

Windows Binary tidybulk_1.2.1.zip

macOS 10.13 (High Sierra) tidybulk_1.2.1.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 3.12 Source Archive