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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
See More
| Suggests | testthat, BiocStyle, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, 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_1.10.0.tar.gz |
| Windows Binary | ideal_1.10.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | ideal_1.10.0.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 |
| Old Source Packages for BioC 3.10 | Source Archive |