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transcript / samsa2

SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
GNU General Public License v3.0
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volcano_plot.R #54

Closed benbechade closed 3 years ago

benbechade commented 3 years ago

R script to visualize differential expression between control and experimental metatranscriptomes. Takes a DESeq output file from the working directory and produces a volcano plot as a .pdf in the same directory. The R package EnhancedVolcano v1.4.0 (https://github.com/kevinblighe/EnhancedVolcano) needs to be installed beforehand on R v>3.6.1. Special characters (e.g. apostrophes) may be the source of issues with the labels on the plot. Also, need to find a way to fit the xlim in a better way.

transcript commented 3 years ago

Adding volcano plot R script created by Benoit Bechade (@benbechade). R script is tested and works with run_DESeq_stats.R output; will need to add EnhancedVolcano to list of R package dependencies.