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ExpHunterSuite

Package for the Comprehensive Analysis of Transcriptomic Data

Bioconductor version: 3.23 · Package version: 1.20.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ExpHunterSuite")

Details

MaintainerJames Perkins <jimrperkins@gmail.com>
AuthorJames Perkins
LicenseMIT + file LICENSE
Downloads rank59
Source branchRELEASE_3_23
biocViewsGeneExpressionWorkflow, Workflow

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Dependencies

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

Suggests: BiocGenerics, biomaRt, EnhancedVolcano, ggupset, naivebayes, optparse, org.Hs.eg.db, org.Mm.eg.db, PerformanceAnalytics, reshape2, testthat (>= 3.0.0)