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ExpHunterSuite

This is the development version of ExpHunterSuite; for the stable release version, see ExpHunterSuite.

Package For The Comprehensive Analysis Of Transcriptomic Data

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ExpHunterSuite")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Details

biocViews GeneExpressionWorkflow, Workflow
Version 1.9.0
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, miRBaseConverter, grDevices, graphics, utils, BiocParallel, MKinfer, matrixStats, rlang, plyr, tidyr, GO.db, Matrix, fastcluster, DOSE, heatmaply, EnhancedVolcano, ggrepel, clusterProfiler
Linking To
Suggests optparse, PerformanceAnalytics, naivebayes, reshape2, TCC, org.Hs.eg.db, org.Mm.eg.db, testthat (>= 3.0.0)
System Requirements
Enhances
URL
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Depends On Me
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Package Archives

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

Source Package
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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