Josh L. Espinoza's repositories
compositional
Compositional data analysis in Python
soothsayer
High-level analysis package for (bio-)informatics
clairvoyance
Feature selection via recursive feature inclusion
ensemble_networkx
Ensemble networks in Python
hive_networkx
Hive plots in Python
fastq_preprocessor
Fastq preprocessor with optional contamination removal. Supports short and long reads.
nif_finder
NMD Inducible Feature Finder
soothsayer_utils
Utility functions for Soothsayer
pykofamsearch
Fast implementation of KofamScan optimized for high-memory systems using PyHmmer
profile
"Hello There"
publications
PDFs for my peer-review scientific publications
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
hierarchical_ensemble_classifier
Customizable scikit-learn compatible hierarchical classifiers.
mapalign
Diffusion map based embedding and alignment
metabolic_niche_space
Metabolic niche space analysis
minpath-nal
MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset
pyhmmsearch
Fast implementation of HMMSEARCH 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.
scikit-hubness
A Python package for hubness analysis and high-dimensional data mining
staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
walkthroughs
Walkthroughs of data analysis
weighted_bootstrap_randomforest
Implementations of weighted bootstrap Random Forest classifier and regressors