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fluentGenomics

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

A plyranges and tximeta workflow


Bioconductor version: Development (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 (from within R, enter citation("fluentGenomics")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.15.0
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)
Linking To
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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_1.15.0.tar.gz
Windows Binary
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/
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