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Nuno Fonseca's Projects

absolut icon absolut

Unconstrained lattice antibody-antigen bindings generator

biophi icon biophi

BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design.

fastq_utils icon fastq_utils

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

flask-boilerplate icon flask-boilerplate

Boilerplate template for a Python Flask application with Flask-SQLAlchemy, Flask-WTF, Fabric, Coverage, and Bootstrap

hts-specs icon hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

irap icon irap

integrated RNA-seq Analysis Pipeline

logchem icon logchem

LogCHEM is a tool for discriminative interactive mining of chemical fragments.

loop_modeling icon loop_modeling

A loop modeling benchmark capture containing the benchmark dataset and benchmarked protocol captures.

propythia icon propythia

Python generic modular semi-automated platform containing functions for the classification of proteins based on their physicochemical properties using ML.

pybadges icon pybadges

A Python library for creating Github-style badges

python-genbadge icon python-genbadge

A library to generate badges for typical checks (flake8, pytest, coverage, etc.)

sadie icon sadie

The Complete Python Antibody Library

sapiens icon sapiens

Sapiens is a human antibody language model based on BERT.

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