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ideal

Interactive Differential Expression AnaLysis

Bioconductor version: Release (3.17)

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 "4.3") 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, ShinyApps, Software, Visualization
Version 1.24.1
In Bioconductor since BioC 3.5 (R-3.4) (6.5 years)
License MIT + file LICENSE
Depends topGO
Imports DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0), heatmaply, plotly, pheatmap, pcaExplorer, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, DT, rentrez, rintrojs, rlang, ggrepel, knitr, rmarkdown, shinyAce, BiocParallel, grDevices, base64enc, methods
Linking To
Suggests testthat, BiocStyle, markdown, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR
System Requirements
Enhances
URL https://github.com/federicomarini/ideal https://federicomarini.github.io/ideal/
Bug Reports https://github.com/federicomarini/ideal/issues
See More
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_1.24.1.tar.gz
Windows Binary ideal_1.24.1.zip
macOS Binary (x86_64) ideal_1.24.1.tgz
macOS Binary (arm64) ideal_1.24.1.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 3.17 Source Archive