Jaime Huerta-Cepas's starred repositories
TreeProfiler
tree visualization for tree + annotation data
Rarefaction
Rarefaction scripts
emapper-benchmark
Raw data and scripts used to benchmark eggnog-mapper. Analysis and additional tests cases are provided as a python notebook.
treematcher
Search flexible patterns within tree structures using regular expression like syntax.
colorization
Automatic colorization using deep neural networks. "Colorful Image Colorization." In ECCV, 2016.
genbank-browser
a genbank file browser using genome-view and biopython. Use example: http://ct.bork.embl.de/ctbrowser/
benchmark-webservice
This repository contains the codebase that runs the webservice to benchmark orthology predictions on a common reference proteome dataset.
eggnog-mapper
Fast genome-wide functional annotation through orthology assignment
TADbit
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
scikit-bio
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
StarCluster
StarCluster is an open source cluster-computing toolkit for Amazon's Elastic Compute Cloud (EC2).