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 (3.23)

The ExpHunterSuite implements a comprehensive protocol for the analysis of transcriptional data using established R packages and combines their results. It covers key steps including differential expression analysis, co-expression analysis, and functional enrichment for RNA-seq data. The package provides interactive R functions as well as command-line scripts that wrap these functions.

Author: James Perkins

Maintainer: James Perkins <jimrperkins at gmail.com>

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

Installation

To install this package, start R (version "4.6") 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

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R Script

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Details

biocViews	GeneExpressionWorkflow, Workflow
Version	1.19.1
License	MIT + file LICENSE
Depends	R (>= 4.1.0)
Imports	AnnotationDbi, annotatr, Biobase, BiocParallel, clusterProfiler, data.table, DESeq2, diffcoexp, DOSE, dplyr, DT, edgeR, enrichit, enrichplot, FactoInvestigate, FactoMineR, fastcluster, GenomicFeatures, GenomicRanges, ggplot2, ggrepel, ggridges, GO.db, graphics, grDevices, heatmaply, knitr, limma, magrittr, Matrix, matrixStats, miRBaseVersions.db, MKinfer, NOISeq, plyr, ReactomePA, rlang, rmarkdown, ROCR, stats, stringr, SummarizedExperiment, tidyr, topGO, tximport, utils, txdbmaker, WGCNA
System Requirements
URL

Suggests	BiocGenerics, biomaRt, EnhancedVolcano, ggupset, naivebayes, optparse, org.Hs.eg.db, org.Mm.eg.db, PerformanceAnalytics, reshape2, testthat (>= 3.0.0)
Linking To
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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	ExpHunterSuite_1.19.1.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (big-sur-arm64)
macOS Binary (sonoma-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