fluentGenomics

DOI: 10.18129/B9.bioc.fluentGenomics    

This is the development version of fluentGenomics; to use it, please install the devel version of Bioconductor.

A plyranges and tximeta workflow

Bioconductor version: Development (3.11)

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 "4.0") and enter:

if (!requireNamespace("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")

 

HTML R Script fluentGenomics
Text   NEWS
Text   LICENSE

Details

biocViews BasicWorkflow, GeneExpressionWorkflow, Workflow
Version 0.99.3
License MIT + file LICENSE
Depends R (>= 4.0)
Imports plyranges(>= 1.7.7), dplyr, SummarizedExperiment, readr, stats, utils
LinkingTo
Suggests knitr, rmarkdown, bookdown, rappdirs, BiocFileCache, DESeq2, limma, ggplot2, tidyr, tximeta(>= 1.4.2), macrophage(>= 1.2.0)
SystemRequirements
Enhances
URL https://github.com/sa-lee/fluentGenomics
BugReports 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_0.99.3.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
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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