Data and code for "The relationship between gene traits and transcription in soil microbial communities varies by environmental stimulus"

This directory contains the code and data used for the manuscript "The relationship between gene traits and transcription in soil microbial communities varies by environmental stimulus".The naming convention of scripts in the `code` directory indicates what step of the process the analysis was run:* `0_*.py` - python scripts used to parse genomic data for codon usage, optimization, and amino acid content. These scripts are set-up to be run on the contigs and gene-calls from JGI.* `1_*.R` - R scripts used to set up data for processing. Data used and generated here can be found in the `data` sub directory* `2_*.R` - R scripts used in analysis and figure generation.<br>Community-level sequence data (i.e. reads, contigs, and annotations) can be found on the JGI Genome Portal (accession numbers listed in manuscript). Metagenome-assembled-genome (MAG) data can be found under this project (https://doi.org/10.6084/m9.figshare.30100291.v1 ). Annotations and gff files can also be found for each MAG in `wv_soil_mags.tar.fz`. CheckM2 output for MAGs can be found in `MAG_quality_report.tsv`. Please note that CheckM2 output file may contain MAGs not included in the analysis due to dereplication.<br>