EngqvistLab

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15 repositories

orgtools
Public
A library to get information on organisms and UniProt identifiers. This includes growth temperature, growth ph, pfam domains, taxonomic lineage.
bioinformatics phylogenetics microbiology bacteria eukaryotes archaea taxonomic-identifiers taxonomic-lineages
Python
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GNU General Public License v3.0
•0•2•0•0•Updated Jun 11, 2024Jun 11, 2024
cheminformatics
Public
Jupyter Notebook
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GNU General Public License v3.0
•0•2•0•2•Updated Aug 15, 2023Aug 15, 2023
UniRep50
Public
A slighlty modified version of the UniRep model
Jupyter Notebook
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GNU General Public License v3.0
•2•5•0•2•Updated Mar 24, 2023Mar 24, 2023
DeepET_reps
Public
An installable library to get DeepET representations.
Jupyter Notebook
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GNU General Public License v3.0
•2•3•1•0•Updated Mar 13, 2022Mar 13, 2022
analyze_1.1.3.15
Public
Code to analyze the 1.1.3.15 experimental data
bioinformatics enzyme biochemistry enzyme-function
HTML
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GNU General Public License v3.0
•0•1•0•0•Updated Apr 9, 2021Apr 9, 2021
yeast_xylanase
Public
A bioinformatic analysis was carried out with the goal of identifying carbohydrate-active enzymes in 332 published yeast genomes.
tree enzyme wood genome-analysis carbohydrates yeast biomass enzyme-function yeastgenome carbohydrate-utilisation
HTML
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GNU General Public License v3.0
•0•0•0•0•Updated Feb 19, 2021Feb 19, 2021
brenparse
Public
A library for parsing out data from the BRENDA database html files
web-scraping biochemistry brenda enzymes brenda-parser enzyme-kinetics
HTML
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GNU General Public License v3.0
•0•1•0•0•Updated Feb 4, 2021Feb 4, 2021
biomark_assays
Public
Enzyme kinetic assays in the Fluidigm Biomark HD instrument
biology high-throughput microfluidics qpcr enzymes enzyme-kinetics
HTML
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GNU General Public License v3.0
•0•0•0•0•Updated Feb 3, 2021Feb 3, 2021
Tome
Public
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
machine-learning bioinformatics microbiology bacteria temperature-data eukaryotes archaea enzymes
Python
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GNU General Public License v3.0
•15•53•5•0•Updated Sep 30, 2020Sep 30, 2020
DeepET
Public
Summary of scripts and results for the manuscript
Jupyter Notebook
•0•0•0•0•Updated Sep 30, 2020Sep 30, 2020
tome_cool
Public
Improve the prediction OGT of psychrophiles
Jupyter Notebook
•0•2•0•0•Updated Mar 3, 2020Mar 3, 2020
Supplemetenary_scripts_datasets_R2LG
Public
This repo contains the supplementary scripts and datasets for Li G, et al, 2019 (https://arxiv.org/abs/1912.08141).
Jupyter Notebook
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GNU General Public License v3.0
•0•2•0•0•Updated Feb 20, 2020Feb 20, 2020
Supplementary_scripts_Tome1.0
Public
Python
•0•0•0•0•Updated Dec 13, 2019Dec 13, 2019
fetch_microbial_growth_temperatures
Public
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.
microbiology temperature-data pasteur bacdive dsmz atcc nctc nies
Python
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GNU General Public License v3.0
•1•6•0•0•Updated Nov 6, 2018Nov 6, 2018
reproducible-reports-init
Public
A template library for use in making research reports/grant proposals follow standard guidelines
Ruby
•0•0•0•0•Updated Apr 27, 2017Apr 27, 2017