bulkAnalyseR: Interactive Shiny App for Bulk Sequencing Data

Given an expression matrix from a bulk sequencing experiment, pre-processes it and creates a shiny app for interactive data analysis and visualisation. The app contains quality checks, differential expression analysis, volcano and cross plots, enrichment analysis and gene regulatory network inference, and can be customised to contain more panels by the user.

Version: 1.1.0
Depends: R (≥ 4.0)
Imports: ggplot2, shiny, gprofiler2, edgeR, DESeq2, stats, ggrepel, utils, RColorBrewer, ComplexHeatmap, circlize, grid, shinyWidgets, shinyjqui, dplyr, magrittr, ggforce, rlang, glue, preprocessCore, matrixStats, noisyr, tibble, ggnewscale, ggrastr, GENIE3, visNetwork, DT, scales, shinyjs, tidyr, shinyLP, UpSetR, stringr, ggVennDiagram
Suggests: rmarkdown, knitr, shinythemes, BiocManager, AnnotationDbi, org.Hs.eg.db, org.Mm.eg.db, readxl, testthat (≥ 3.0.0)
Published: 2022-12-15
Author: Ilias Moutsopoulos [aut, cre], Eleanor Williams [aut, ctb], Irina Mohorianu [aut, ctb]
Maintainer: Ilias Moutsopoulos <im383 at cam.ac.uk>
BugReports: https://github.com/Core-Bioinformatics/bulkAnalyseR/issues
License: GPL-2
URL: https://github.com/Core-Bioinformatics/bulkAnalyseR
NeedsCompilation: no
Materials: README
CRAN checks: bulkAnalyseR results

Documentation:

Reference manual: bulkAnalyseR.pdf
Vignettes: A beginner's guide to creating a bulkAnalyseR app from a GEO dataset
bulkAnalyseR: Integrating multi-omics or external data
bulkAnalyseR: An accessible, interactive pipeline for analysing and sharing bulk sequencing results

Downloads:

Package source: bulkAnalyseR_1.1.0.tar.gz
Windows binaries: r-devel: bulkAnalyseR_1.1.0.zip, r-release: bulkAnalyseR_1.1.0.zip, r-oldrel: bulkAnalyseR_1.1.0.zip
macOS binaries: r-release (arm64): bulkAnalyseR_1.1.0.tgz, r-oldrel (arm64): bulkAnalyseR_1.1.0.tgz, r-release (x86_64): bulkAnalyseR_1.1.0.tgz
Old sources: bulkAnalyseR archive

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