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scikit-learn Public
Forked from scikit-learn/scikit-learnscikit-learn: machine learning in Python
Python BSD 3-Clause "New" or "Revised" License UpdatedSep 5, 2024 -
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ReAmBaP Public
Remove ambiguous base pairs from FASTA files
Python GNU General Public License v3.0 UpdatedAug 8, 2024 -
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kidera-atchley Public
Forked from vadimnazarov/kidera-atchleyLoad biophysicochemical properties of amino acids, Kidera factors and Atchley factors into R and Python in only a single line.
Python MIT License UpdatedJul 4, 2024 -
SparCC Public
Forked from dlegor/SparCCSparCC is a Python module for calculating correlations in compositional data
Python Other UpdatedFeb 22, 2024 -
UPEC_pop_study_Norfolk Public
Material for "UPEC Population Structure and Antimicrobial Susceptibility in Norfolk, UK"
Jupyter Notebook UpdatedMar 24, 2023 -
HybridRateModel Public
Forked from rfjoni/ParticleModelHybrid machine learning framework for modelling
Python UpdatedNov 21, 2022 -
short-read-dilutions-calc Public
A script I use for quickly converting Qubit readings from DNA extractions into dilutions I need for submitting my samples for short read sequencing.
Python UpdatedMay 20, 2022 -
ATPScan Public
Analysis tools used for scanning ATP production in my E. coli UTI89 model in ScrumPy
Python UpdatedMay 10, 2022 -
ScrumPy-Notebook Public
Learn metabolic modelling and using ScrumPy for modelling.
HTML GNU General Public License v3.0 UpdatedMar 15, 2022 -
tuatara Public
Reconstruct and handle many genome-scale metabolic models in ScrumPy
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LPScanner Public
Rapid linear programme scanning and batch processing for ScrumPy
Python GNU General Public License v3.0 UpdatedFeb 7, 2022 -
ST-literature-search Public
Literature search tool for publications relating to E. coli sequence types
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AbxRxPro Public
Visualise your isolate's antibiotic resistance profile
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Enrichment-Plot Public
Map gene presence/absence results as metabolic pathways
Python GNU General Public License v3.0 UpdatedAug 17, 2021 -
MobileGeneticElementDatabase Public
Forked from KatariinaParnanen/MobileGeneticElementDatabaseContains a fasta format database of a large variety of mobile genetic elements and an annotation file
UpdatedAug 16, 2021 -
EcoliCollection Public
Scripts used for handling my E coli assemblies collection
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Deep-Learning-to-predict-resistance-to-Fluoroquinolone-antibiotics Public
Forked from VadimDu/Deep-Learning-to-predict-resistance-to-Fluoroquinolone-antibioticsIn this interactive tutorial we will preform machine-learning (deep learning) analysis of bacterial DNA gyrase/topoisomerase in order to predict resistance to Fluoroquinolones antibiotics. We will …
Jupyter Notebook MIT License UpdatedJun 21, 2021 -
FASTAfromBLAST Public
Extract FASTA sequences of regions of genome assemblies from NCBI BLAST alignments
Python GNU General Public License v3.0 UpdatedApr 29, 2021 -
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escher Public
Forked from zakandrewking/escherBuild, share, and embed visualizations of metabolic pathways.
JavaScript Other UpdatedMar 30, 2021 -
EMBLtoFASTA Public
Convert EMBL files to FASTA
Python GNU General Public License v3.0 UpdatedMar 30, 2021 -
ATP-Data-Plot Public
Visualise ATP over time under antibiotic challenge from the literature
Python MIT License UpdatedMar 30, 2021 -
fasta_from_ena Public
Download FASTA files from ENA using an XML report of a search.
Python GNU General Public License v3.0 UpdatedMar 29, 2021 -
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