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Bioconductor - tidybulk (development version)

tidybulk

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

Brings transcriptomics to the tidyverse

Bioconductor version: Development (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")

# 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")

Details biocViews AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics Version 1.21.0 In Bioconductor since BioC 3.11 (R-4.0) (5 years) License GPL-3 Depends R (>= 4.4.0), 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.

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