ExpHunterSuite
This is the released version of ExpHunterSuite; for the devel version, see ExpHunterSuite.
Package for the Comprehensive Analysis of Transcriptomic Data
Bioconductor version: Release (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("ExpHunterSuite")):James Perkins. ExpHunterSuite: Package for the Comprehensive Analysis of Transcriptomic Data. doi:10.18129/B9.bioc.ExpHunterSuite, R package version 1.20.0, https://bioconductor.org/packages/ExpHunterSuite.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5.5 years) |
| 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 |
See More
| Suggests | BiocGenerics, biomaRt, EnhancedVolcano, ggupset, naivebayes, optparse, org.Hs.eg.db, org.Mm.eg.db, PerformanceAnalytics, reshape2, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ExpHunterSuite_1.20.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| 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 |