ideal
This is thereleased version of ideal; for the devel version, seeideal.
Interactive Differential Expression AnaLysis
Bioconductor version: Release (3.22)
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: 0000-0003-3252-7758
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")BiocManager::install("ideal")For older versions of R, please refer to the appropriateBioconductor 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 | 2.4.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (8.5 years) |
| License | MIT + fileLICENSE |
| 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/idealhttps://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
FollowInstallation instructions to use this package in your R session.
| Source Package | ideal_2.4.0.tar.gz |
| Windows Binary (x86_64) | ideal_2.4.0.zip (64-bit only) |
| macOS Binary (x86_64) | ideal_2.4.0.tgz |
| macOS Binary (arm64) | ideal_2.4.0.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 |