ideal

Interactive Differential Expression AnaLysis

Bioconductor version: Release (3.20)

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. Support for reproducibility of the whole analysis is provided by means of a template report which gets automatically compiled and can be stored/shared.

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, ImmunoOncology, QualityControl, RNASeq, ReportWriting, Sequencing, ShinyApps, Software, Visualization
Version	2.0.0
In Bioconductor since	BioC 3.5 (R-3.4) (7.5 years)
License	MIT + file LICENSE
Depends	topGO
Imports	DESeq2, SummarizedExperiment, mosdef(>= 1.1.0), GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0), heatmaply, plotly, pheatmap, 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, graphics, base64enc, methods, utils, stats
System Requirements
URL	https://github.com/federicomarini/ideal https://federicomarini.github.io/ideal/
Bug Reports	https://github.com/federicomarini/ideal/issues

Suggests	testthat, BiocStyle, markdown, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, htmltools, 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_2.0.0.tar.gz
Windows Binary (x86_64)	ideal_2.0.0.zip (64-bit only)
macOS Binary (x86_64)	ideal_2.0.0.tgz
macOS Binary (arm64)	ideal_2.0.0.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