DOI: 10.18129/B9.bioc.fluentGenomics    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see fluentGenomics.

A plyranges and tximeta workflow

Bioconductor version: 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")):


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HTML R Script fluentGenomics
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biocViews BasicWorkflow, GeneExpressionWorkflow, Workflow
Version 1.0.1
License MIT + file LICENSE
Depends R (>= 4.0)
Imports plyranges(>= 1.7.7), dplyr, SummarizedExperiment, readr, stats, utils
Suggests knitr, rmarkdown, bookdown, rappdirs, BiocFileCache, DESeq2, limma, ggplot2, tidyr, tximeta(>= 1.4.2), macrophage(>= 1.2.0)
URL https://github.com/sa-lee/fluentGenomics
BugReports https://github.com/sa-lee/fluentGenomics/issues
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Source Package fluentGenomics_1.0.1.tar.gz
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Package Short Url https://bioconductor.org/packages/fluentGenomics/
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