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cancer-cell-line-mhc-alleles

Cell line HLA types and neoepitope catalog from TCLP

coronavirus-sequences

cov-2-mutations-by-lineage

Quick analysis to associate SARS-Cov-2 spike mutations with pangolin lineages using GISAID data

datacache

Helpers for transparently downloading datasets

ensembl-data

Mirror of GTF and FASTA data from the Ensembl FTP servers

files

Reference genomes and related files used across repos and analyses

gene-lists

Gene lists related to cancer immunotherapy

gtfparse

Parsing tools for GTF (gene transfer format) files

hla-e-ligands

List of published peptide ligands for HLA-E

isovar

Assembly of RNA reads to determine the effect of a cancer mutation on protein sequence

mhc2-data

Class II MHC data

mhc2flurry

MHC class II binding predictor, under development

mhcdouble

Class II MHC binding and antigen processing prediction

mhcflurry

Peptide-MHC I binding affinity prediction

mhcflurry-motifs

Motifs for MHC I alleles as predicted by MHCflurry

mhcflurry-web

Webapp for MHCflurry predictor

mhcnames

All the fun and adventure of MHC naming, now in Python

mhctools

Python interface to running command-line and web-based MHC binding predictors

mutexp

Predict expression of cancer mutations from simple DNA features such as DNA variant allele-frequency

neoantigen-vaccine-pipeline

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines

openvax-integration-tests

Test which use the whole python genomics / immunology software stack that can be included with each project

openvax-project-template

Template for a new OpenVax Python project

openvax.github.io

openvax.github.io

ott-wu-2017-data

Machine readable data from "An Immunogenic Personal Neoantigen Vaccine for Melanoma Patients"

pepdata

Python interface to amino acid properties and IEDB

pepnet

Neural networks for amino acid sequences

phipkit

PhIP-seq data analysis workflow

predicting-ase-from-dna-features

Predicting allele-specific expression of somatic mutations from DNA features

proteopt

Common interface to protein design tools and structure predictors

pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl