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: | 1.0.0 |
| 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 |
| Suggests: | rmarkdown, knitr, shinythemes, BiocManager, AnnotationDbi, org.Hs.eg.db, org.Mm.eg.db, readxl, testthat (≥ 3.0.0) |
| Published: | 2022-04-07 |
| 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 |
| Package source: | bulkAnalyseR_1.0.0.tar.gz |
| Windows binaries: | r-devel: bulkAnalyseR_1.0.0.zip, r-release: bulkAnalyseR_1.0.0.zip, r-oldrel: bulkAnalyseR_1.0.0.zip |
| macOS binaries: | r-release (arm64): bulkAnalyseR_1.0.0.tgz, r-oldrel (arm64): bulkAnalyseR_1.0.0.tgz, r-release (x86_64): bulkAnalyseR_1.0.0.tgz, r-oldrel (x86_64): bulkAnalyseR_1.0.0.tgz |
| Old sources: | bulkAnalyseR archive |
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