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tidybulk

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

Brings transcriptomics to the tidyverse


Bioconductor version: Development (3.19)

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 "4.4") 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")
Overview of the tidybulk package HTML R Script
Reference Manual PDF

Details

biocViews AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.15.2
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL-3
Depends R (>= 4.1.0), ttservice (>= 0.3.6)
Imports tibble, readr, dplyr (>= 1.1.0), magrittr, tidyr, stringi, stringr, rlang, purrr, tidyselect, preprocessCore, stats, parallel, utils, lifecycle, scales, SummarizedExperiment, GenomicRanges, methods, S4Vectors, crayon, Matrix
System Requirements
URL https://github.com/stemangiola/tidybulk
Bug Reports https://github.com/stemangiola/tidybulk/issues
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, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, igraph, EGSEA, IRanges, here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS, pkgconfig
Linking To
Enhances
Depends On Me
Imports Me tidyomics
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_1.15.2.tar.gz
Windows Binary tidybulk_1.15.2.zip
macOS Binary (x86_64) tidybulk_1.15.2.tgz
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
Bioc Package Browser https://code.bioconductor.org/browse/tidybulk/
Package Short Url https://bioconductor.org/packages/tidybulk/
Package Downloads Report Download Stats