tidybulk
This is thereleased version of tidybulk; for the devel version, seetidybulk.
Brings transcriptomics to the tidyverse
Bioconductor version: Release (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")BiocManager::install("tidybulk")For older versions of R, please refer to the appropriateBioconductor 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 |
| Side-by-side comparison with standard interfaces | HTML | R Script |
| Reference Manual |
Details
| biocViews | AssayDomain,Clustering,DifferentialExpression,GeneExpression,Infrastructure,Normalization,QualityControl,RNASeq,Sequencing,Software,Transcription,Transcriptomics |
| Version | 2.0.1 |
| In Bioconductor since | BioC 3.11 (R-4.0) (5.5 years) |
| License | GPL-3 |
| 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 |
| 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,widyr,clusterProfiler,msigdbr,DESeq2,broom,survival,boot,betareg,tidyHeatmap,pasilla,ggrepel,devtools,functional,survminer,tidySummarizedExperiment,markdown,uwot,matrixStats,preprocessCore,igraph,EGSEA,IRanges,here,glmmSeq,pbapply,pbmcapply,lme4,glmmTMB,MASS,pkgconfig,enrichplot,patchwork,airway |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | tidyomics |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | tidybulk_2.0.1.tar.gz |
| Windows Binary (x86_64) | tidybulk_2.0.1.zip |
| macOS Binary (x86_64) | tidybulk_2.0.1.tgz |
| macOS Binary (arm64) | tidybulk_2.0.1.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 |
| Old Source Packages for BioC 3.22 | Source Archive |