Hallam Lab

University of British Columbia, Vancouver, British Columbia, Canada

Pinned Repositories

FAST
FAST Aligner
Language:C++5 3 21
FragGeneScanPlus
Scalable high-throughput short-read open reading frame prediction
Language:C12 8 1311
HivePanelExplorer
An interactive and explorative visualization tool in D3 based on hive plots built for complex networks.
Language:Python9 5 03
LAST-Plus
Parallel implementation of the LAST aligner
Language:C++18 6 103
LCAStar
Alternative taxonomic consensus algorithms based on the NCBI taxonomy tree
Language:HTML14 3 23
metapathways2
MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds
Language:Python33 13 10314
mp_tutorial
A repository of notes, code, slides, and resources for the MetaPathways tutorial being held February 2014 at UBC.
Language:R19 10 419
pathway2vec
Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction
Language:Python16 4 13
SABer
SAG Anchored Binner
Language:Python3 3 82
TreeSAPP
A Python package for gene-centric taxonomic and functional classification using phylogenetic placement
Language:Python26 7 714

Hallam Lab's Repositories

hallamlab/TreeSAPP
A Python package for gene-centric taxonomic and functional classification using phylogenetic placement
Language:Python26 7 714
hallamlab/pathway2vec
Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction
Language:Python16 4 13
hallamlab/LCAStar
Alternative taxonomic consensus algorithms based on the NCBI taxonomy tree
Language:HTML14 3 23
hallamlab/FragGeneScanPlus
Scalable high-throughput short-read open reading frame prediction
Language:C12 8 1311
hallamlab/HivePanelExplorer
An interactive and explorative visualization tool in D3 based on hive plots built for complex networks.
Language:Python9 5 03
hallamlab/mlLGPR
Metabolic pathway inference using multi-label classification with rich pathway features
Language:Python7 2 3
hallamlab/samsum
A light-weight python package for summarizing sequence coverage from SAM and BAM files
Language:Python6 4 103
hallamlab/FAST
FAST Aligner
Language:C++5 3 21
hallamlab/MetaPathwaysGUI
Language:C++3 4 25
hallamlab/SABer
SAG Anchored Binner
Language:Python3 3 82
hallamlab/FabFos
A python-driven fosmid processing pipeline
Language:Python1 2 63
hallamlab/Limes-x
Language:Python1 0 3
hallamlab/RefPkgs
Repository for TreeSAPP reference packages
Language:Python1 4 43
hallamlab/reMap
reMap: relabeling metabolic pathway data with groups to improve prediction outcomes
Language:Python1 4 00
hallamlab/sgRNAble
Language:Python1 5 41
hallamlab/SOFA
Short-ORF Functional Annotation Pipeline
Language:C++1 4 30
hallamlab/BLOB
Code and data repository for the BLOB manuscript
0 4 00
hallamlab/chap
CHAP: Modeling Metabolic Pathways as Groups (with Augmentation)
Language:Python0 5 01
hallamlab/leADS
leADS: improved metabolic pathway inference based on active dataset subsampling
Language:Python0 4 01
hallamlab/lighting_system_design_2024
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"
Language:Python0 4 00
hallamlab/TaxonomicDistinctness
Language:HTML0 3 00
hallamlab/Fosmid-walk
Language:Python0 0
hallamlab/Limes-compute-modules
Language:Python0 0
hallamlab/MAGSplitter
Standalone script to split a Metapathways metagenome output by MAGs
Language:Python0 0
hallamlab/MetaTaxa
5 0
hallamlab/NESAP_marine_heatwaves
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.
Language:RMarkdown1
hallamlab/OMZ_SAG_Compendium_Figures
3 0
hallamlab/python_starter_template
Language:Python0 0
hallamlab/sagex
Language:C6 24
hallamlab/triUMPF
Metabolic pathway inference using non-negative matrix factorization with community detection
Language:Python4 21