ideal
This is the released version of ideal; for the devel version, see ideal.
Interactive Differential Expression AnaLysis
Bioconductor version: Release (3.23)
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]
Maintainer: Federico Marini <marinif at uni-mainz.de>
citation("ideal")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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, ShinyApps, Software, Visualization |
| Version | 2.6.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 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_2.6.0.tar.gz |
| Windows Binary (x86_64) | ideal_2.6.0.zip |
| macOS Binary (big-sur-x86_64) | ideal_2.6.0.tgz |
| macOS Binary (sonoma-arm64) | ideal_2.6.0.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 |