ideal

DOI: 10.18129/B9.bioc.ideal    

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

Interactive Differential Expression AnaLysis

Bioconductor version: Development (3.9)

This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package.

Author: Federico Marini [aut, cre] (<https://orcid.org/0000-0003-3252-7758>)

Maintainer: Federico Marini <marinif at uni-mainz.de>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ideal", version = "3.9")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ideal")

 

HTML R Script ideal User's Guide
PDF   Reference Manual
Text   LICENSE

Details

biocViews DifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, QualityControl, RNASeq, ReportWriting, Sequencing, Software, Visualization
Version 1.7.0
In Bioconductor since BioC 3.5 (R-3.4) (1.5 years)
License MIT + file LICENSE
Depends topGO
Imports DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0), d3heatmap, pheatmap, pcaExplorer, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, DT, rentrez, rintrojs, knitr, rmarkdown, shinyAce, BiocParallel, grDevices, methods
LinkingTo
Suggests testthat, BiocStyle, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR
SystemRequirements
Enhances
URL https://github.com/federicomarini/ideal https://federicomarini.github.io/ideal/
BugReports https://github.com/federicomarini/ideal/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package ideal_1.7.0.tar.gz
Windows Binary ideal_1.7.0.zip
Mac OS X 10.11 (El Capitan) ideal_1.7.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ideal
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ideal
Package Short Url http://bioconductor.org/packages/ideal/
Package Downloads Report Download Stats

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