ideal

DOI: 10.18129/B9.bioc.ideal    

This is the development version of ideal; for the stable release version, see ideal.

Interactive Differential Expression AnaLysis

Bioconductor version: Development (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>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews	DifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, ImmunoOncology, QualityControl, RNASeq, ReportWriting, Sequencing, Software, Visualization
Version	1.23.0
In Bioconductor since	BioC 3.5 (R-3.4) (5.5 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
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_1.23.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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	https://bioconductor.org/packages/ideal/
Package Downloads Report	Download Stats