DOI: 10.18129/B9.bioc.tidybulk  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see tidybulk.

Brings transcriptomics to the tidyverse

Bioconductor version: 3.16

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")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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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


biocViews AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.10.1
In Bioconductor since BioC 3.11 (R-4.0) (3 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
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
URL https://github.com/stemangiola/tidybulk
BugReports https://github.com/stemangiola/tidybulk/issues
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Build Report  

Package Archives

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

Source Package tidybulk_1.10.1.tar.gz
Windows Binary tidybulk_1.10.1.zip
macOS Binary (x86_64) tidybulk_1.10.1.tgz
macOS Binary (arm64) tidybulk_1.10.1.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/
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