hallamlab Goto Github PK

beer

R tutorials

blob

Code and data repository for the BLOB manuscript

chap

CHAP: Modeling Metabolic Pathways as Groups (with Augmentation)

data_wrangling

Notes on basic metagenomic data wrangling

fabfos

A python-driven fosmid processing pipeline

fast

FAST Aligner

fastlsa

An implementation of the Local Similarity Statistics using an approximate p-value upper bound

fosmid-walk

fraggenescanplus

Scalable high-throughput short-read open reading frame prediction

hivepanelexplorer

An interactive and explorative visualization tool in D3 based on hive plots built for complex networks.

json-js

JSON in JavaScript

koonkie

Hadoop framework for metagenomic processing

last

UBC Hallam Lab modifications on the popular sequence alignment software LAST (http://last.cbrc.jp/)

last-plus

Parallel implementation of the LAST aligner

lcastar

Alternative taxonomic consensus algorithms based on the NCBI taxonomy tree

leads

leADS: improved metabolic pathway inference based on active dataset subsampling

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"

limes-compute-modules

limes-x

magsplitter

Standalone script to split a Metapathways metagenome output by MAGs

metapathways

A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information

metapathways2

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds

metapathwaysgui

metataxa

mllgpr

Metabolic pathway inference using multi-label classification with rich pathway features

mp_2_5_supplement

Source code of the supplementary material of the Oxford Bioinformatics MetaPathways v2.5 paper.

mp_tutorial

A repository of notes, code, slides, and resources for the MetaPathways tutorial being held February 2014 at UBC.

network-robustness

Python modules and classes to run robustness simulations on networks

omz_sag_compendium_figures

pathway2vec

Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction