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ExpHunterSuite

Package For The Comprehensive Analysis Of Transcriptomic Data


Bioconductor version: Release (3.18)

The ExpHunterSuite implements a comprehensive protocol for the analysis of transcriptional data using established *R* packages and combining their results. It covers all key steps in DEG detection, CEG detection and functional analysis for RNA-seq data. It has been implemented as an R package containing functions that can be run interactively. In addition, it also contains scripts that wrap the functions and can be run directly from the command line.

Author: James Perkins [aut, cre] , Pedro Seoane Zonjic [aut] , Fernando Moreno Jabato [aut] , José Córdoba Caballero [aut] , Elena Rojano Rivera [aut] , Rocio Bautista Moreno [aut] , M. Gonzalo Claros [aut] , Isabel Gonzalez Gayte [aut], Juan Antonio García Ranea [aut]

Maintainer: James Perkins <jimrperkins at gmail.com>

Citation (from within R, enter citation("ExpHunterSuite")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ExpHunterSuite")

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("ExpHunterSuite")
The Expression Hunter Suite HTML R Script
NEWS Text
LICENSE Text

Details

biocViews GeneExpressionWorkflow, Workflow
Version 1.10.0
License MIT + file LICENSE
Depends R (>= 4.1.0)
Imports ReactomePA, limma, edgeR, NOISeq, biomaRt, topGO, diffcoexp, DT, ggplot2, stringr, WGCNA, dplyr, AnnotationDbi, BiocGenerics, enrichplot, rmarkdown, stats, Biobase, DESeq2, ROCR, data.table, knitr, magrittr, SummarizedExperiment, miRBaseVersions.db, grDevices, graphics, utils, BiocParallel, MKinfer, matrixStats, ggupset, rlang, plyr, tidyr, GO.db, Matrix, fastcluster, DOSE, heatmaply, EnhancedVolcano, ggrepel, clusterProfiler, GenomicRanges, GenomicFeatures, tximport, annotatr, ggridges, FactoInvestigate, FactoMineR
System Requirements
URL
See More
Suggests optparse, PerformanceAnalytics, naivebayes, reshape2, org.Hs.eg.db, org.Mm.eg.db, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ExpHunterSuite_1.10.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/ExpHunterSuite
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ExpHunterSuite
Package Short Url https://bioconductor.org/packages/ExpHunterSuite/
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