fluentGenomics

This is the released version of fluentGenomics; for the devel version, see fluentGenomics.

A plyranges and tximeta workflow

Platform availability badge Ranking badge Support activity badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.fluentGenomics

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0003-1179-8436 , Michael Love [aut, ctb]

Maintainer: Stuart Lee <stuart.andrew.lee at gmail.com>

Citation (from within R, enter citation("fluentGenomics")):

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BasicWorkflow, GeneExpressionWorkflow, Workflow

Version 1.22.0

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

Suggests knitr, rmarkdown, bookdown, rappdirs, BiocFileCache, DESeq2, limma, ggplot2, tidyr, tximeta(>= 1.4.2), macrophage(>= 1.2.0)

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package fluentGenomics_1.22.0.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