Jamie Morton's repositories
multiomics_network
Network visualizations for bacterial species and metabolites from microbiome data
benchmark-mae
Benchmarking repository for microbe-metabolite interactions
BERT-pytorch
Google AI 2018 BERT pytorch implementation
conda-recipes
conda recipes for bioinformatic tools like blast+, infernal, etc.
DEICODE
toolbox for mapping data association to ecology in low-density & noisy metagenomic data
emperor
Emperor a tool for the analysis and visualization of large microbial ecology datasets
empress-feedstock
Conda recipe for empress
Genomic-ULMFiT
ULMFiT for Genomic Sequence Data
microbiome-patterns
Scripts and data to accompany Marsland, Cui and Mehta "A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns," bioRxiv 622829 (2019)
mmvec-feedstock
A conda-smithy repository for mmvec.
networkx
Official NetworkX source code repository.
picrust2
Code, unit tests, and tutorials for running PICRUSt2
poisson-cat
Compute poisson differentials based on categorical sample metadata
pytorch-transformers
👾 A library of state-of-the-art pretrained models for Natural Language Processing (NLP)
PyTorch_GBW_LM
PyTorch Language Model for 1-Billion Word (LM1B / GBW) Dataset
q2-picrust2
QIIME2 plugin for PICRUSt2
random-qp
Code and data to accompany Mehta, Cui, Wang and Marsland, "Constrained optimization as ecological dynamics with applications to random quadratic programming in high dimensions," arXiv:1809.04221 (2019).
rankratioviz
Visualize differentially ranked features (taxa, metabolites, ...) in tandem with log ratios of their sample abundances
stray
Multinomial Logistic-Normal Linear Regression Models
torchdiffeq
Differentiable ODE solvers with full GPU support and O(1)-memory backpropagation.