Josh L. Espinoza

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

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

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

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

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

soothsayer. High-level analysis package for (bio-)informatics

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

clairvoyance. AutoML simultaneous bayesian hyperparameter optimization and feature selection

kegg_pathway_profiler. 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 within Python and via CLI executables.

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

projects. Various research projects

hive_networkx. Hive plots in Python

genopype. Architecture for creating bash pipelines, in particular, for bioinformatics

genomic_neighborhood. Versatile command-line tool designed to create publication quality genomic neighborhood plots built on top of DnaFeaturesViewer

nif_finder. NMD Inducible Feature Finder

soothsayer_utils. Utility functions for Soothsayer

metacoag-nal. 🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs (NAL mod with Pyrodigal and PyHMMSearch)

MetagenomicKG. Python

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

nf-core-fastqpreprocessor. Fastq preprocessor with optional contamination removal implemented in NextFlow. Supports short and long reads.

pipelines. Automated informatics pipelines with consistent directory structures

nf-modules. Genomics modules for NextFlow

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

leviathan-case-study-plastisphere. Leviathan case study using the Plastisphere dataset