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tidybulk

Brings transcriptomics to the tidyverse

Bioconductor version: Release (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>

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

Installation

To install this package, start R (version "4.3") 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 feature abundance HTML R Script
Manuscript code - transcriptional signature identification HTML R Script
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 1.12.0
In Bioconductor since BioC 3.11 (R-4.0) (3.5 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
Linking To
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
System Requirements
Enhances
URL https://github.com/stemangiola/tidybulk
Bug Reports https://github.com/stemangiola/tidybulk/issues
See More
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_1.12.0.tar.gz
Windows Binary tidybulk_1.12.0.zip
macOS Binary (x86_64) tidybulk_1.12.0.tgz
macOS Binary (arm64) tidybulk_1.12.0.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