fluentGenomics

A plyranges and tximeta workflow

Bioconductor version: Release (3.17)

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 <lee.s at wehi.edu.au>

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

Installation

To install this package, start R (version "4.3") 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	1.12.0
License	MIT + file LICENSE
Depends	R (>= 4.0)
Imports	plyranges(>= 1.7.7), dplyr, SummarizedExperiment, readr, stats, utils
Linking To
Suggests	knitr, rmarkdown, bookdown, rappdirs, BiocFileCache, DESeq2, limma, ggplot2, tidyr, tximeta(>= 1.4.2), macrophage(>= 1.2.0)
System Requirements
Enhances
URL	https://github.com/sa-lee/fluentGenomics
Bug Reports	https://github.com/sa-lee/fluentGenomics/issues

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_1.12.0.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/
Package Downloads Report	Download Stats