ideal

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see ideal.

Interactive Differential Expression AnaLysis


Bioconductor version: 3.10

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 (version "3.6") and enter:


if (!require("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")
ideal User's Guide HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, ImmunoOncology, QualityControl, RNASeq, ReportWriting, Sequencing, Software, Visualization
Version 1.10.0
In Bioconductor since BioC 3.5 (R-3.4) (7 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, ggrepel, knitr, rmarkdown, shinyAce, BiocParallel, grDevices, base64enc, methods
System Requirements
URL https://github.com/federicomarini/ideal https://federicomarini.github.io/ideal/
Bug Reports https://github.com/federicomarini/ideal/issues
See More
Suggests testthat, BiocStyle, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package ideal_1.10.0.tar.gz
Windows Binary ideal_1.10.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) ideal_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ideal
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ideal
Bioc Package Browser https://code.bioconductor.org/browse/ideal/
Package Short Url https://bioconductor.org/packages/ideal/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive