Pinned Repositories
mhcflurry
Peptide-MHC I binding affinity prediction
mhctools
Python interface to running command-line and web-based MHC binding predictors
proteopt
Common interface to protein design tools and structure predictors
varcode
Library for manipulating genomic variants and predicting their effects
varlens
commandline manipulation of genomic variants and NGS reads
alaya
Python library to expose status info or debug output to interested users via a web server embedded in the process
genomisc
miscellaneous analysis tools for next generation sequencing datasets
pyopen
load csv, excel, json, hdf5, and pickle files into an ipython session
sefara
practical dataset management
yabul
Yet Another Bioinformatics Utilities Library
timodonnell's Repositories
timodonnell/pyopen
load csv, excel, json, hdf5, and pickle files into an ipython session
timodonnell/sefara
practical dataset management
timodonnell/yabul
Yet Another Bioinformatics Utilities Library
timodonnell/alaya
Python library to expose status info or debug output to interested users via a web server embedded in the process
timodonnell/genomisc
miscellaneous analysis tools for next generation sequencing datasets
timodonnell/manuscript_ab_epitope_interaction
timodonnell/tahini
experiments with apache scrunch
timodonnell/bamread
Bam to Pandas DataFrame, quickly
timodonnell/eventlearn
feature extraction from irregularly-spaced timeseries
timodonnell/gcloud-psql-cron
Send pg_dump backups to gcloud storage buckets
timodonnell/immuno
Predicting immunogenicity of short peptides
timodonnell/LSUV-keras
Simple implementation of the LSUV initialization in keras
timodonnell/mhcgnomes
Parsing MHC nomenclature in the wild
timodonnell/mhcpred
MHC Binding Prediction
timodonnell/nametagday
timodonnell/OmegaFold
OmegaFold Release Code
timodonnell/openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
timodonnell/openfold-dev
Scratch space for experiments with OpenFold
timodonnell/pepnet
Neural networks for amino acid sequences
timodonnell/phip-stat
Analysis tools for PhIP-seq experiments
timodonnell/ProteinMPNN
This fork modifies ProteinMPNN to be (mostly) usable as a Python library
timodonnell/proteinpile
Manage protein design experiments
timodonnell/pyfaidx
pyfaidx: efficient pythonic random access to fasta subsequences
timodonnell/RFDesign
This fork modifies RFDesign to be (mostly) usable as a Python library
timodonnell/RFdiffusion
Code for running RFdiffusion
timodonnell/scikit-learn
scikit-learn: machine learning in Python
timodonnell/sparkbox
tools that use Spark's MLlib
timodonnell/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/timodonnell.github.io
timodonnell/website