ideal
This is the development version of ideal; for the stable release version, see ideal.
Interactive Differential Expression AnaLysis
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Federico Marini <marinif at uni-mainz.de>
citation("ideal")):
Installation
To install this package, start R (version "4.5") 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")| ideal User's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, ImmunoOncology, QualityControl, RNASeq, ReportWriting, Sequencing, ShinyApps, Software, Visualization |
| Version | 2.1.0 |
| 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 |
See More
| 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_2.1.0.tar.gz |
| Windows Binary (x86_64) | |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/ideal/ |
| Package Short Url | https://bioconductor.org/packages/ideal/ |
| Package Downloads Report | Download Stats |