To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ideal")

In most cases, you don't need to download the package archive at all.

ideal

DOI: 10.18129/B9.bioc.ideal

Interactive Differential Expression AnaLysis

Bioconductor version: Release (3.5)

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]

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

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ideal")

Documentation

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

Details

biocViews DifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, QualityControl, RNASeq, ReportWriting, Sequencing, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.5 (R-3.4) (0.5 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, plyr, 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
BugReports https://github.com/federicomarini/ideal/issues
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package ideal_1.0.0.tar.gz
Windows Binary ideal_1.0.0.zip
Mac OS X 10.11 (El Capitan) ideal_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ideal
Package Short Url http://bioconductor.org/packages/ideal/
Package Downloads Report Download Stats

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