This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see tidybulk.
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")
):
To install this package, start R (version "4.0") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("tidybulk")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("tidybulk")
HTML | R Script | 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 |
Reference Manual |
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) (1 year) |
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 |
LinkingTo | |
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 |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
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Build Report |
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 |
Package Short Url | https://bioconductor.org/packages/tidybulk/ |
Package Downloads Report | Download Stats |
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