All the input data for the scripts described can be found here.
The data for the jupyter notebooks are here
This repository contains the code as used for the following sections
- plot heatmaps for nullitetra, all genes (not just triads)
- get expression for nullitetras 1:1:1 triads
- add dominance category to nullitetra 1:1:1 triad expression
- plot and stats for A vs B vs D for nullitetras and dominance categories
Details in Jupyter notebook
Expressed genes within the Azhurnaya developmental time course (209 samples) and Chinese Spring no stress (123 samples).
Details in Jupyter notebook
- differential expression all tissues compared to anther
- differential expression all tissues compared to awns
- differential expression all tissues compared to embryo
- differential expression all tissues compared to endosperm
- differential expression all tissues compared to flag leaf blade
- differential expression all tissues compared to flag leaf sheath
- differential expression all tissues compared to glumes
- differential expression all tissues compared to grain hard
- differential expression all tissues compared to grain milk
- differential expression all tissues compared to internode
- differential expression all tissues compared to leaf blades excl flag
- differential expression all tissues compared to leaf ligule
- differential expression all tissues compared to leaf sheaths excl flag
- differential expression all tissues compared to peduncle
- differential expression all tissues compared to root apical meristem
- differential expression all tissues compared to seedling aerial tissues
- differential expression all tissues compared to shoot apical meristem
- differential expression all tissues compared to shoot axis
- differential expression all tissues compared to spike
- differential expression all tissues compared to spikelets
- differential expression all tissues compared to stigma ovary
- after differential expression analysis filter differentially expressed genes for padj < 0.05
- after filtering padj < 0.05 summarise differentially expressed genes
The browser is available here
Details in Jupyter notebook
Details in Jupyter notebook
Details in Jupyter notebook
Details in Jupyter notebook
The scripts used for this section are in various repositories:
Clarite is available here
- Calculate sliding window of Transposable Element density upstream of genes
- Calculate average lengths and distances from start site of Transposable Elements including statistical tests
- Script for analysis of TE presence/absence based on homoeolog expression bias categories.
- Script for analysis of TE presence/absence based on homoeolog expression bias variation categories.
- Script for analysis of TE family enrichment based on homoeolog expression bias variation categories.
- Analyse TFBS categories according to triad movement including statistical tests
- Filter unique FIMO hits only - step 1
- Generate TFBS categories based on occurrence in triads
- Filter unique FIMO hits only - step 2
- Run FIMO to identify TFBS in promoters
- [MAFFT alignment](https://github.com/TGAC/bioruby-polyploid- tools/blob/master/bin/mafft_triads.rb.)
- Script to obtain Chinese Spring No-Stress analysis of Ka/Ks ratios for syntenic 1:1:1 triads.
- Script to obtain Azhurnaya development analysis of Ka/Ks ratios for syntenic 1:1:1 triads.
- Script to obtain Chinese Spring No-Stress analysis of Ka/Ks ratios for non-syntenic 1:1:1 triads.
- Script to obtain Azhurnaya development analysis of Ka/Ks ratios for non-syntenic 1:1:1 triads.
- WGCNA combine studies filter normalise samples for abiotic.R
- WGCNA combine studies filter normalise samples for disease.R
- WGCNA combine studies filter normalise samples for grain.R
- WGCNA combine studies filter normalise samples for leaf.R
- WGCNA combine studies filter normalise samples for root.R
- WGCNA combine studies filter normalise samples for spike.R
- WGCNA determine threshold for abiotic.R
- WGCNA determine threshold for disease.R
- WGCNA determine threshold for grain.R
- WGCNA determine threshold for leaf.R
- WGCNA determine threshold for root.R
- WGCNA determine threshold for spike.R
- WGCNA run WGCNA abiotic.R
- WGCNA run WGCNA disease.R
- WGCNA run WGCNA grain.R
- WGCNA run WGCNA leaf.R
- WGCNA run WGCNA root.R
- WGCNA run WGCNA spike.R
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