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alaya

Python library to expose status info or debug output to interested users via a web server embedded in the process

bamread

Bam to Pandas DataFrame, quickly

eventlearn

feature extraction from irregularly-spaced timeseries

gcloud-psql-cron

Send pg_dump backups to gcloud storage buckets

genomisc

miscellaneous analysis tools for next generation sequencing datasets

immuno

Predicting immunogenicity of short peptides

ipython

Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.

lsuv-keras

Simple implementation of the LSUV initialization in keras

manuscript_ab_epitope_interaction

mhcgnomes

Parsing MHC nomenclature in the wild

mhcpred

MHC Binding Prediction

nametagday

omegafold

OmegaFold Release Code

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

openfold-dev

Scratch space for experiments with OpenFold

pepnet

Neural networks for amino acid sequences

phip-stat

Analysis tools for PhIP-seq experiments

proteinmpnn

This fork modifies ProteinMPNN to be (mostly) usable as a Python library

proteinpile

Manage protein design experiments

pyfaidx

pyfaidx: efficient pythonic random access to fasta subsequences

pyopen

load csv, excel, json, hdf5, and pickle files into an ipython session

rfdesign

This fork modifies RFDesign to be (mostly) usable as a Python library

rfdiffusion

Code for running RFdiffusion

scikit-learn

scikit-learn: machine learning in Python

sefara

practical dataset management

sparkbox

tools that use Spark's MLlib

tahini

experiments with apache scrunch

theano

Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It can use GPUs and perform efficient symbolic differentiation.

timodonnell.github.io

website