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
| Maintainer | James Perkins <jimrperkins@gmail.com> |
| Author | James Perkins |
| License | MIT + file LICENSE |
| Downloads rank | 59 |
| Source branch | RELEASE_3_23 |
| biocViews | GeneExpressionWorkflow, 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)