Hallam Lab

All

44 repositories

NESAP_marine_heatwaves
Public
This is the code repository for our manuscript highlighting the effects of marine heatwaves on food webs and particle export in the Northeast Subarctic Pacific Ocean.
0•0•0•0•Updated Oct 30, 2024Oct 30, 2024
TreeSAPP
Public
A Python package for gene-centric taxonomic and functional classification using phylogenetic placement
phylogenetics microbial-genomics bioinformatics
Python
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GNU General Public License v3.0
•4•25•18•3•Updated Sep 3, 2024Sep 3, 2024
SABer
Public
SAG Anchored Binner
Python
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GNU General Public License v3.0
•2•3•6•1•Updated Sep 3, 2024Sep 3, 2024
samsum
Public
A light-weight python package for summarizing sequence coverage from SAM and BAM files
bioinformatics sequence-alignment
Python
•
GNU General Public License v3.0
•3•5•8•1•Updated Sep 3, 2024Sep 3, 2024
FabFos
Public
A python-driven fosmid processing pipeline
Python
•
GNU General Public License v3.0
•3•1•5•1•Updated Jul 30, 2024Jul 30, 2024
LCAStar
Public
Alternative taxonomic consensus algorithms based on the NCBI taxonomy tree
HTML
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GNU General Public License v3.0
•3•14•0•0•Updated May 29, 2024May 29, 2024
lighting_system_design_2024
Public
Git repository containing the code and associated high-throughput screening data published in the article "An automated high-throughput lighting-system for screening photosynthetic microorganisms in plate-based formats"
Python
•0•0•0•0•Updated Feb 16, 2024Feb 16, 2024
python_starter_template
Public
Python
•
GNU General Public License v3.0
•1•0•0•0•Updated Oct 17, 2023Oct 17, 2023
Fosmid-walk
Public
Python
•1•0•0•0•Updated Oct 5, 2023Oct 5, 2023
Limes-compute-modules
Public
Python
•2•0•0•0•Updated Sep 14, 2023Sep 14, 2023
Limes-x
Public
Python
•1•1•3•0•Updated Aug 6, 2023Aug 6, 2023
MAGSplitter
Public
Standalone script to split a Metapathways metagenome output by MAGs
Python
•1•0•0•0•Updated Jul 27, 2023Jul 27, 2023
mlLGPR
Public
Metabolic pathway inference using multi-label classification with rich pathway features
bioinformatics metagenomics logistic-regression multi-label-learning pathway-prediction metacyc biocyc pathway-tools
Python
•
GNU General Public License v3.0
•0•6•1•1•Updated Jul 6, 2023Jul 6, 2023
OMZ_SAG_Compendium_Figures
Public
0•0•0•0•Updated Mar 22, 2023Mar 22, 2023
MetaPathwaysGUI
Public
C++
•0•3•0•0•Updated Jan 19, 2023Jan 19, 2023
sgRNAble
Public
Python
•
GNU General Public License v3.0
•1•1•3•2•Updated Dec 8, 2022Dec 8, 2022
MetaTaxa
Public
0•0•0•0•Updated Aug 2, 2022Aug 2, 2022
RefPkgs
Public
Repository for TreeSAPP reference packages
Python
•
GNU General Public License v3.0
•3•1•2•1•Updated Apr 16, 2022Apr 16, 2022
leADS
Public
leADS: improved metabolic pathway inference based on active dataset subsampling
bioinformatics metagenomics metabolic-network multi-label-learning multi-label-classfications metacyc metabolic-pathways acquisition-functions biocyc pathway-tools
Python
•
GNU General Public License v3.0
•1•0•0•0•Updated Nov 16, 2021Nov 16, 2021
chap
Public
CHAP: Modeling Metabolic Pathways as Groups (with Augmentation)
bioinformatics metagenomics topic-modeling pathway-analysis metabolic-network metabolic-reconstruction pathway-prediction metacyc metabolic-pathways pathway-enrichment-analysis
Python
•
GNU General Public License v3.0
•1•0•0•0•Updated Nov 8, 2021Nov 8, 2021
reMap
Public
reMap: relabeling metabolic pathway data with groups to improve prediction outcomes
groups bioinformatics embeddings topic-modeling multi-label-classification bags centroid multi-label-learning metacyc metabolic-pathways
Python
•
GNU General Public License v3.0
•0•1•0•0•Updated Nov 8, 2021Nov 8, 2021
triUMPF
Public
Metabolic pathway inference using non-negative matrix factorization with community detection
bioinformatics metagenomics multi-label-classification metabolic-reconstruction non-negative-matrix-factorization multi-label-learning pathway-prediction metacyc metabolic-pathways subnetwork
Python
•
GNU General Public License v3.0
•1•0•1•0•Updated Sep 19, 2021Sep 19, 2021
BLOB
Public
Code and data repository for the BLOB manuscript
0•0•0•0•Updated Aug 9, 2021Aug 9, 2021
pathway2vec
Public
Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction
bioinformatics deep-learning metapath embedding metacyc heterogeneous-information-networks biocyc pathway-tools pathway-prediction
Python
•
GNU General Public License v3.0
•3•15•1•0•Updated Jul 8, 2021Jul 8, 2021
HivePanelExplorer
Public
An interactive and explorative visualization tool in D3 based on hive plots built for complex networks.
Python
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Other
•11•9•0•0•Updated Nov 2, 2020Nov 2, 2020
TaxonomicDistinctness
Public
HTML
•0•0•0•0•Updated Feb 13, 2020Feb 13, 2020
sagex
Public
C
•0•0•3•0•Updated Dec 18, 2018Dec 18, 2018
SOFA
Public
Short-ORF Functional Annotation Pipeline
C++
•0•1•0•0•Updated Aug 28, 2018Aug 28, 2018
FAST
Public
FAST Aligner
C++
•1•5•2•0•Updated Mar 21, 2017Mar 21, 2017
FragGeneScanPlus
Public
Scalable high-throughput short-read open reading frame prediction
C
•11•12•6•4•Updated Jan 13, 2017Jan 13, 2017