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clairvoyance

Feature selection via recursive feature inclusion

compositional

Compositional data analysis in Python

ensemble_networkx

Ensemble networks in Python

fastq_preprocessor

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

flexible-clustering

Clustering for arbitrary data and dissimilarity function

genomic_neighborhood

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

genopype

Architecture for creating bash pipelines, in particular, for bioinformatics

hierarchical_ensemble_classifier

Customizable scikit-learn compatible hierarchical classifiers.

hive_networkx

Hive plots in Python

jolespin.github.io

mapalign

Diffusion map based embedding and alignment

metagenomickg

nif_finder

NMD Inducible Feature Finder

pipelines

Automated informatics pipelines with consistent directory structures

profile

"Hello There"

projects

Various research projects

publications

PDFs for my peer-review scientific publications

pyhmmsearch

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

pykofamsearch

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

scikit-bio

scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.

soothsayer

High-level analysis package for (bio-)informatics

soothsayer_utils

Utility functions for Soothsayer

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

veba

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

walkthroughs

Walkthroughs of data analysis

weighted_bootstrap_randomforest

Implementations of weighted bootstrap Random Forest classifier and regressors