Pinned Repositories
gtfparse
Parsing tools for GTF (gene transfer format) files
isovar
Assembly of RNA reads to determine the effect of a cancer mutation on protein sequence
mhcflurry
Peptide-MHC I binding affinity prediction
mhctools
Python interface to running command-line and web-based MHC binding predictors
neoantigen-vaccine-pipeline
Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines
pepdata
Python interface to amino acid properties and IEDB
pyensembl
Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
topiary
Predict mutated T-cell epitopes from sequencing data
varcode
Library for manipulating genomic variants and predicting their effects
vaxrank
Ranked vaccine peptides for personalized cancer immunotherapy
OpenVax's Repositories
openvax/topiary
Predict mutated T-cell epitopes from sequencing data
openvax/pepnet
Neural networks for amino acid sequences
openvax/varlens
commandline manipulation of genomic variants and NGS reads
openvax/gene-lists
Gene lists related to cancer immunotherapy
openvax/mhcdouble
Class II MHC binding and antigen processing prediction
openvax/ott-wu-2017-data
Machine readable data from "An Immunogenic Personal Neoantigen Vaccine for Melanoma Patients"
openvax/mhc2-data
Class II MHC data
openvax/sahin-2017-data
Machine readable data from "Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer"
openvax/vaxrank-paper-2018
Repository for updated Vaxrank paper
openvax/mutexp
Predict expression of cancer mutations from simple DNA features such as DNA variant allele-frequency
openvax/openvax-integration-tests
Test which use the whole python genomics / immunology software stack that can be included with each project
openvax/openvax-project-template
Template for a new OpenVax Python project
openvax/predicting-ase-from-dna-features
Predicting allele-specific expression of somatic mutations from DNA features
openvax/typechecks
Type checking helpers for Python