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R notebook with the differential expression analysis during drought stress among bioenergy grass Miscanthus species

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jjdevega/miscanthus_drought_rnaseq

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DOI

Transcriptional differences among four Miscanthus species (M. sacchariflorus, M. sinensis, M. x giganteus, and a triploid M. sacchariflorus X M. sinensis) under three water regimes: control, waterlogging (saturated) and drought (low soil mousture).

This repository contains the code of the RNA-seq analysis from our paper, which is available in X.

**The R notebook (rnaseq_analysis.Rmd) is fully run here with all the figures: https://jjdevega.github.io/miscanthus_drought_rnaseq/

Repository contents

The R markdown raw file is complete_analysis.Rmd in the main folder, that is all you need together with the files in the INPUT folder: The counts are available in the text table, and the phenotypes (metadata) is also in a txt file. All the other files can be generated during the execution of the R notebook.

Functional annotation of the Miscanthus sinensis genome

The folder 'input' contains a functional annotation of the M. sinensis genome v.7.1 available in phytozome using Blast2GO. The folder contains the GO terms in the format for topGO that the analysis uses.

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R notebook with the differential expression analysis during drought stress among bioenergy grass Miscanthus species

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