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https://github.com/cropgeeks/barleypantranscriptome

Barley pan-transcriptome paper -- analysis code

https://github.com/cropgeeks/barleypantranscriptome

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Barley pan-transcriptome paper -- analysis code

Basic Info
  • Host: GitHub
  • Owner: cropgeeks
  • Language: Perl
  • Default Branch: main
  • Size: 91.8 KB
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Created almost 3 years ago · Last pushed over 1 year ago
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Readme

README.md

Barley pan-transcriptome paper -- analysis code

This repository contains the analysis scripts used in the barley pan-transcriptome paper.

These are organised as follows: - scripts/geneClustering/Gene.cluster.filter.R: this script is used to filter gene duplication clusters. It reads gene clustering results and gene info (coordinates and strand) as input files. It outputs a table of gene clusters in tandem, cluster range and number of genes in the cluster. - scripts/MorexAtlas: contains all scripts used for the construction of the Morex gene expression atlas and for hosting it on the EORNA web infrastructure. - scripts/TFBS: contains the scripts used for analysing the transcription factor binding sites and plotting the results from this.

There is a separate README that details the construction of the PanBaRT20 RTD.

Scripts used in the network construction and analysis are found here.

Scripts used for the phenology gene analysis are hosted in a separate github repository here.

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  • Name: cropgeeks
  • Login: cropgeeks
  • Kind: organization

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