Genomics modules for NextFlow

A comprehensive clustering toolkit with advanced tree cutting, visualization, and network analysis capabilities.

Python package for compositional data analysis including CLR/ILR, proportionality, partial correlation with basis shrinkage, and visualizations.

A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

Fastq preprocessor with optional contamination removal. Supports short and long reads.

Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for (pan)genome-resolved metagenomics and metatranscriptomics

PyExeggutor is a simple wrapper for the subprocess module to run shell commands in Python

Python package for association, differential, clustered, and sample-specific ensemble networks. Direct support for compositional data analysis. Additional capabilities for feature engineering.

Fast implementation of HMMSEARCH optimized for high-memory systems using PyHMMER

Fast implementation of KofamScan optimized for high-memory systems using PyHMMER

A pathway profiling tool designed for traversing metabolic pathway graphs, identifying most complete paths based on an evaluation set of KEGG orthologs (KO), and generalized for internal usage with…

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Customizable scikit-learn compatible hierarchical classifiers.

AutoML simultaneous bayesian hyperparameter optimization and feature selection

A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes. Implemented in NextFlow.

Core utility functions and objects for VEBA

Fastq preprocessor with optional contamination removal implemented in NextFlow. Supports short and long reads.

PDFs for my peer-review scientific publications

Nested rule and definition evaluator