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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
| 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 |
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 |