openvax/mhctools

Stars
78
Rank 409,982 (Top 9 %)
Language
Python
License
Apache License 2.0
Created over 9 years ago
Updated about 1 year ago

openvax/mhctools

openvax

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

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

varcode

Library for manipulating genomic variants and predicting their effects

neoantigen-vaccine-pipeline

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines

Jupyter Notebook

vaxrank

Ranked vaccine peptides for personalized cancer immunotherapy

pepdata

Python interface to amino acid properties and IEDB

topiary

Predict mutated T-cell epitopes from sequencing data

isovar

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

pepnet

Neural networks for amino acid sequences

varlens

commandline manipulation of genomic variants and NGS reads

gene-lists

Gene lists related to cancer immunotherapy

tcga-immune-deconvolution

Immune deconvolution of publicly available TCGA expression data

Jupyter Notebook

mhcnames

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

datacache

Helpers for transparently downloading datasets

cancer-cell-line-mhc-alleles

Cell line HLA types and neoepitope catalog from TCLP

Jupyter Notebook

mhcdouble

Class II MHC binding and antigen processing prediction

ott-wu-2017-data

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

Jupyter Notebook

mhc2-data

Class II MHC data

Jupyter Notebook

sahin-2017-data

Machine readable data from "Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer"

vaxrank-paper-2018

Repository for updated Vaxrank paper

proteopt

Common interface to protein design tools and structure predictors

mhcflurry-motifs

Motifs for MHC I alleles as predicted by MHCflurry

mhc2flurry

MHC class II binding predictor, under development

Jupyter Notebook

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

Jupyter Notebook