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

Need some help? Ask on the Bioconductor Support site!

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

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

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