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ideal

Interactive Differential Expression AnaLysis

Bioconductor version: 3.23 · Package version: 2.6.0

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.

Installation

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

BiocManager::install("ideal")

Details

MaintainerFederico Marini <marinif@uni-mainz.de>
AuthorFederico Marini [aut, cre] (ORCID: <https://orcid.org/0000-0003-3252-7758>)
LicenseMIT + file LICENSE
URLhttps://github.com/federicomarini/ideal, https://federicomarini.github.io/ideal/
Bug Reportshttps://github.com/federicomarini/ideal/issues
Downloads rank481
Source branchRELEASE_3_23
biocViewsDifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, ImmunoOncology, QualityControl, RNASeq, ReportWriting, Sequencing, ShinyApps, Software, Visualization

Documentation

Download

Dependencies

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

Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, htmltools, edgeR