fluentGenomics
A plyranges and tximeta workflow
Bioconductor version: Release (3.19)
An extended workflow using the plyranges and tximeta packages for fluent genomic data analysis. Use tximeta to correctly import RNA-seq transcript quantifications and summarize them to gene counts for downstream analysis. Use plyranges for clearly expressing operations over genomic coordinates and to combine results from differential expression and differential accessibility analyses.
Author: Stuart Lee [aut, cre] 
, Michael Love [aut, ctb]
Maintainer: Stuart Lee <stuart.andrew.lee at gmail.com>
citation("fluentGenomics")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("fluentGenomics")
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("fluentGenomics")| fluentGenomics | HTML | R Script |
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BasicWorkflow, GeneExpressionWorkflow, Workflow |
| Version | 1.16.0 |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0) |
| Imports | plyranges(>= 1.7.7), dplyr, SummarizedExperiment, readr, stats, utils |
| System Requirements | |
| URL | https://github.com/sa-lee/fluentGenomics |
| Bug Reports | https://github.com/sa-lee/fluentGenomics/issues |
See More
| Suggests | knitr, rmarkdown, bookdown, rappdirs, BiocFileCache, DESeq2, limma, ggplot2, tidyr, tximeta(>= 1.4.2), macrophage(>= 1.2.0) |
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| Depends On Me | |
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Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fluentGenomics_1.16.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/fluentGenomics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/fluentGenomics |
| Package Short Url | https://bioconductor.org/packages/fluentGenomics/ |
| Package Downloads Report | Download Stats |