tidybulk
Brings transcriptomics to the tidyverse
Bioconductor version: 3.23 · Package version: 2.2.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tidybulk")Details
| Maintainer | Stefano Mangiola <mangiolastefano@gmail.com> |
| Author | Stefano Mangiola [aut, cre], Maria Doyle [ctb] |
| License | GPL-3 |
| URL | https://github.com/stemangiola/tidybulk |
| Bug Reports | https://github.com/stemangiola/tidybulk/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | AssayDomain, Clustering, DifferentialExpression, GeneExpression, Infrastructure, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/tidybulk/ |
Citation
From within R, enter citation("tidybulk"):
Stefano Mangiola. tidybulk: Brings transcriptomics to the tidyverse. doi:10.18129/B9.bioc.tidybulk, R package version 2.2.0, https://bioconductor.org/packages/tidybulk.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- tidybulk: An R tidy framework for modular transcriptomic data analysis
- Side-by-side comparison with standard interfaces
Download
Follow the installation instructions to use this package in your R session.
| Source package | tidybulk_2.2.0.tar.gz |
| Windows binary (x86_64) | tidybulk_2.2.0.zip |
| macOS binary (arm64) | tidybulk_2.2.0.tgz |
| macOS binary (x86_64) | tidybulk_2.2.0.tgz |
Dependencies
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
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, fastmatch, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, preprocessCore, igraph, EGSEA, IRanges, here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS, pkgconfig, enrichplot, patchwork, airway