https://github.com/jokergoo/gseatraining

https://github.com/jokergoo/gseatraining

Last synced: 24 days ago
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• Host: GitHub
• URL: https://github.com/jokergoo/gseatraining
• Owner: jokergoo
• Created: 2023-01-29T15:58:36.000Z (almost 2 years ago)
• Default Branch: master
• Last Pushed: 2024-01-26T09:03:47.000Z (10 months ago)
• Last Synced: 2024-05-09T07:45:30.942Z (6 months ago)
• Language: HTML
• Homepage: https://jokergoo.github.io/GSEAtraining
• Size: 77 MB
• Stars: 14
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: readme.md

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README

        


First make sure you have the following two packages installed:

- **devtools**

- **BiocManager**

If you don't have them yet, install them from CRAN.

Then install the **GSEAtraining** package for this course:

```r

library(devtools)

# this may take ~30 min because it builds all practice materials

install_github("jokergoo/GSEAtraining", dependencies = TRUE, 

	build_vignettes = TRUE)

```

You should also update the following two packages from GitHub because

the updates are only available on the bioc devel branch:

```r

install_github("jokergoo/simona")

install_github("jokergoo/BioCartaImage")

install_github("jokergoo/rGREAT")

```

If you have errors with installing dependency packages, try to install them manually:

```r

BiocManager::install(c("DBI", "DT", "RSQLite", "htmltools", "shiny", "AnnotationDbi", "matrixStats",

    "GO.db", "org.Hs.eg.db", "KEGGREST", "clusterProfiler", "msigdbr",

    "reactome.db", "AnnotationHub",

    "Orthology.eg.db", "microbenchmark", "ReactomePA", "DOSE", "org.Ss.eg.db",

    "CePa", "eulerr", "rGREAT", "goseq", "GSVA", "simplifyEnrichment", 

    "enrichplot", "ggplot2", "ComplexHeatmap", "circlize", "genefilter"))

install.packages("https://jokergoo.github.io/GSEAtraining_0.99.1.tar.gz", repo = NULL, type = "source")

```

The practice materials are also available at https://jokergoo.github.io/GSEAtraining/.

**Do not use it for commercial purpose.**