Bioconductor version: Release (3.17)
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")
):
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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ExpHunterSuite")
HTML | R Script | The Expression Hunter Suite |
Text | NEWS | |
Text | LICENSE |
biocViews | GeneExpressionWorkflow, Workflow |
Version | 1.8.0 |
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 |
LinkingTo | |
Suggests | optparse, PerformanceAnalytics, naivebayes, reshape2, TCC, org.Hs.eg.db, org.Mm.eg.db, testthat (>= 3.0.0) |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me |
Follow Installation instructions to use this package in your R session.
Source Package | ExpHunterSuite_1.8.0.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/ |
Package Downloads Report | Download Stats |
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