https://github.com/mattbixley/nesi_r

example R code for the various NeSI platforms
https://github.com/mattbixley/nesi_r

Last synced: 7 days ago
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example R code for the various NeSI platforms

• Host: GitHub
• URL: https://github.com/mattbixley/nesi_r
• Owner: MattBixley
• License: mit
• Created: 2024-07-10T22:24:22.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2024-08-20T21:30:41.000Z (3 months ago)
• Last Synced: 2024-08-21T03:38:51.300Z (3 months ago)
• Language: R
• Size: 747 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# nesi_r

example R code for the various NeSI platforms, will eventually turn into a quarto website

### Bioninformatics

`bioinformatics.r`

example script's both slurm and R for running some bioinformatics specific packages and functions based on the R-bundle-bioinformatics modules on Mahuika

From https://genomicsaotearoa.github.io/RNA-seq-workshop/

tests with `limma`, `edgeR` and `DESeq2` which utilises Bioconductor and BiocManager

### Geospatial

as above for Geospatial work which relies heavily on GDAL, proj, sp and other system libraries and R packages

terra needs a version update, blocks raster loading?

### devtools/remotes

R packages key for doing installation from non CRAN spaces, specifically github

`library(devtools)`

`library(remotes)`

### ggplot

`plotting.r`

test code for plotting, making sure RStudio/RStudio Server drivers are compatible with `cairo` ie all the module above. Failure is that the plot window doesn;t open.

##########

Below - use File > New > ...... and create dummy docs, HTML should work PDFs require work, possibly the pandoc module

 

### Markdown

examples and test ability to output to html AND pdf, pdfs will require miktex or other latex engine

### Quarto

qaurto likely similar requirements

### Shiny

### Jupyter Notebooks

maybe ;-)