Alan's repositories
TCRdock
python tools for TCR:peptide-MHC modeling and analysis
NeoFuse
NeoFuse is a user-friendly pipeline for the prediction of fusion neoantigens from tumor RNA-seq data.
fastbook
The fastai book, published as Jupyter Notebooks
TITAN
T Cell Receptor Specificity Prediction with Bimodal Attention Networks
neofox
Annotation of mutated peptide sequences (mps) with published or novel potential neo-epitope descriptors
provis
Official code repository of "BERTology Meets Biology: Interpreting Attention in Protein Language Models."
SeqDesign
Protein design and variant prediction using autoregressive generative models
USMPep
Major Histocompatibility Complex (MHC) Binding Affinity Prediction
rbm-mhc
Python3 script to implement RBM-MHC - a predictor for class I antigen presentation - described in Bravi et al. 2020 (https://www.biorxiv.org/content/10.1101/2020.04.25.061069v1)
tcr_classifier
Predicting T Cell Receptor Specificity with Deep Learning
bumps
Data fitting with uncertainty analysis
pyemd
Fast EMD for Python: a wrapper for Pele and Werman's C++ implementation of the Earth Mover's Distance metric
zstr
A C++ header-only ZLib wrapper
beast-mcmc
Bayesian Evolutionary Analysis Sampling Trees
jarad.github.com
Github userpage
ompg-public
Loop simulations for Outer Membrane Protein G
sparsepp
A fast, memory efficient hash map for C++
boost.simd
Portable SIMD computation library - To be proposed as a Boost library
minicsv
Automatically exported from code.google.com/p/minicsv
CRoaring
Roaring bitmaps in C (and C++)
rhdfs
A package that allows R developers to use Hadoop HDFS
RHadoop
RHadoop
rmr2
A package that allows R developer to use Hadoop MapReduce
rhbase
A package that allows R developers to use Hadoop HBase
zookeeper-leader-election
A simple library for Apache ZooKeeper leader election