https://github.com/nellore/mr1

explores alternative splicing of MR1 across GTEx
https://github.com/nellore/mr1

Last synced: 11 months ago
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explores alternative splicing of MR1 across GTEx

• Host: GitHub
• URL: https://github.com/nellore/mr1
• Owner: nellore
• License: mit
• Created: 2018-01-18T21:11:47.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2018-04-23T23:08:26.000Z (over 7 years ago)
• Last Synced: 2024-12-30T00:24:50.673Z (about 1 year ago)
• Language: Mathematica
• Size: 6.69 MB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# MR1

This repository contains scripts that reproduce a plot of the distributions of _MR1_ exon 4 inclusion-to-skip ratios across GTEx tissues starting [Snaptron](https://academic.oup.com/bioinformatics/article/34/1/114/4101942) queries. Refer to `query_and_generate_table.sh` for how the queries were generated. The _MR1_ transcript NM_001531 includes exon 4 and is distinguished by two junctions, the average of whose coverages we call A; NM_001195000 excludes exon 4 and is distinguished by one junction, whose coverage we call B. `query_and_generate_table.sh` outputs `isoform_ratio_table.tsv`, which lists for each GTEx sample our proxy `A / B` for the isoform ratio as well as corresponding tissue labels. The notebook `plots.nb` generates the final plot `histogramDensityPlot.pdf` from `isoform_ratio_table.tsv`. We ran it with Mathematica 10.4.1 and saved a PDF transcript as `plots.pdf`.