OpenVax

pyensembl

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

mhcflurry

Peptide-MHC I binding affinity prediction

gtfparse

Parsing tools for GTF (gene transfer format) files

mhctools

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

varcode

Library for manipulating genomic variants and predicting their effects

neoantigen-vaccine-pipeline

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines

vaxrank

Ranked vaccine peptides for personalized cancer immunotherapy

pepdata

Python interface to amino acid properties and IEDB

isovar

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

tcga-immune-deconvolution

Immune deconvolution of publicly available TCGA expression data

mhcnames

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

cancer-cell-line-mhc-alleles

Cell line HLA types and neoepitope catalog from TCLP

datacache

Helpers for transparently downloading datasets

mhcflurry-web

Webapp for MHCflurry predictor

cov-2-mutations-by-lineage

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

mhc2flurry

MHC class II binding predictor, under development

mhcflurry-motifs

Motifs for MHC I alleles as predicted by MHCflurry

proteopt

Common interface to protein design tools and structure predictors

phipkit

PhIP-seq data analysis workflow

coronavirus-sequences

ensembl-data

Mirror of GTF and FASTA data from the Ensembl FTP servers

files

Reference genomes and related files used across repos and analyses

hla-e-ligands

List of published peptide ligands for HLA-E

openvax.github.io

openvax.github.io

sarscov2-brazil-seqdata

Exploring the sequencing data from SARSCoV2 patient SPBR1 in Brazil

sarscov2-primers

Genome amplification primers for SARS-CoV2 from ARTIC v1 with modification to 2019_76_RIGHT

sercol

Serializable collection class with filtering and grouping methods

serializable

Base class with serialization methods for user-defined Python objects

synoptiko

Summary report of somatic mutations from cancer DNA sequencing data

vafster

Extract allelic fractions from all the horrible ways VCFs encode allele counts