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analyze_1.1.3.15

Code to analyze the 1.1.3.15 experimental data

biomark_assays

Enzyme kinetic assays in the Fluidigm Biomark HD instrument

brenparse

A library for parsing out data from the BRENDA database html files

cheminformatics

deepet

Summary of scripts and results for the manuscript

deepet_reps

An installable library to get DeepET representations.

fetch_microbial_growth_temperatures

Code to go with the https://doi.org/10.1101/271569 publication. Downloads html pages from culture-collection centers and mines these for growth temperature data.

orgtools

A library to get information on organisms and UniProt identifiers. This includes growth temperature, growth ph, pfam domains, taxonomic lineage.

reproducible-reports-init

A template library for use in making research reports/grant proposals follow standard guidelines

supplementary_scripts_tome1.0

supplemetenary_scripts_datasets_r2lg

This repo contains the supplementary scripts and datasets for Li G, et al, 2019 (https://arxiv.org/abs/1912.08141).

tome

A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima

tome_cool

Improve the prediction OGT of psychrophiles

unirep50

A slighlty modified version of the UniRep model

yeast_xylanase

A bioinformatic analysis was carried out with the goal of identifying carbohydrate-active enzymes in 332 published yeast genomes.