ideal

DOI: 10.18129/B9.bioc.ideal    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see ideal.

Interactive Differential Expression AnaLysis

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

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

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("ideal")

 

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

Details

biocViews	DifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, ImmunoOncology, QualityControl, RNASeq, ReportWriting, Sequencing, Software, Visualization
Version	1.6.1
In Bioconductor since	BioC 3.5 (R-3.4) (2 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_1.6.1.tar.gz
Windows Binary	ideal_1.6.1.zip
Mac OS X 10.11 (El Capitan)	ideal_1.6.1.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