tidybulk

This is the released version of tidybulk; for the devel version, see tidybulk.

Brings transcriptomics to the tidyverse

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DOI: 10.18129/B9.bioc.tidybulk

Bioconductor version: Release (3.22)

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 "4.5") 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")

Overview of the tidybulk package HTML R Script

Side-by-side comparison with standard interfaces 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 2.0.1

In Bioconductor since BioC 3.11 (R-4.0) (5.5 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

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, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, preprocessCore, igraph, EGSEA, IRanges, here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS, pkgconfig, enrichplot, patchwork, airway

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Build Report Build Report

Package Archives

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

Source Package tidybulk_2.0.1.tar.gz

Windows Binary (x86_64) tidybulk_2.0.1.zip

macOS Binary (x86_64) tidybulk_2.0.1.tgz

macOS Binary (arm64) tidybulk_2.0.1.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 3.22 Source Archive