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 (3.21)

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] ORCID: 0000-0003-4108-096X , Pedro Seoane Zonjic [aut] ORCID: 0000-0002-3020-1415 , Fernando Moreno Jabato [aut] ORCID: 0000-0001-7498-1962 , José Córdoba Caballero [aut] ORCID: 0000-0002-1821-5742 , Elena Rojano Rivera [aut] ORCID: 0000-0002-2678-710X , Rocio Bautista Moreno [aut] ORCID: 0000-0003-1685-8119 , M. Gonzalo Claros [aut] ORCID: 0000-0002-0112-3550 , Isabel Gonzalez Gayte [aut], Juan Antonio García Ranea [aut] ORCID: 0000-0003-0327-1837

Maintainer: James Perkins <jimrperkins at gmail.com>

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

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("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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpressionWorkflow, Workflow
Version	1.15.0
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

Suggests	optparse, PerformanceAnalytics, naivebayes, reshape2, org.Hs.eg.db, org.Mm.eg.db, testthat (>= 3.0.0)
Linking To
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Depends On Me
Imports Me
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Package Archives

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

Source Package	ExpHunterSuite_1.15.0.tar.gz
Windows Binary (x86_64)
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/
Package Downloads Report	Download Stats