OpenVax (@openvax)
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Top repositories

1

pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Python
338
star
2

mhcflurry

Peptide-MHC I binding affinity prediction
Python
171
star
3

gtfparse

Parsing tools for GTF (gene transfer format) files
Python
92
star
4

mhctools

Python interface to running command-line and web-based MHC binding predictors
Python
78
star
5

varcode

Library for manipulating genomic variants and predicting their effects
Python
75
star
6

neoantigen-vaccine-pipeline

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines
Jupyter Notebook
68
star
7

vaxrank

Ranked vaccine peptides for personalized cancer immunotherapy
Python
49
star
8

pepdata

Python interface to amino acid properties and IEDB
Python
48
star
9

topiary

Predict mutated T-cell epitopes from sequencing data
Python
27
star
10

isovar

Assembly of RNA reads to determine the effect of a cancer mutation on protein sequence
Python
22
star
11

pepnet

Neural networks for amino acid sequences
Python
20
star
12

varlens

commandline manipulation of genomic variants and NGS reads
Python
19
star
13

gene-lists

Gene lists related to cancer immunotherapy
13
star
14

tcga-immune-deconvolution

Immune deconvolution of publicly available TCGA expression data
Jupyter Notebook
11
star
15

mhcnames

All the fun and adventure of MHC naming, now in Python
Python
10
star
16

datacache

Helpers for transparently downloading datasets
Python
5
star
17

cancer-cell-line-mhc-alleles

Cell line HLA types and neoepitope catalog from TCLP
Jupyter Notebook
4
star
18

mhcdouble

Class II MHC binding and antigen processing prediction
Python
4
star
19

ott-wu-2017-data

Machine readable data from "An Immunogenic Personal Neoantigen Vaccine for Melanoma Patients"
Jupyter Notebook
4
star
20

mhc2-data

Class II MHC data
Jupyter Notebook
2
star
21

sahin-2017-data

Machine readable data from "Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer"
1
star
22

vaxrank-paper-2018

Repository for updated Vaxrank paper
TeX
1
star
23

proteopt

Common interface to protein design tools and structure predictors
Python
1
star
24

mhcflurry-motifs

Motifs for MHC I alleles as predicted by MHCflurry
Python
1
star
25

mhc2flurry

MHC class II binding predictor, under development
Jupyter Notebook
1
star
26

mhcflurry-web

Webapp for MHCflurry predictor
CSS
1
star
27

cov-2-mutations-by-lineage

Quick analysis to associate SARS-Cov-2 spike mutations with pangolin lineages using GISAID data
Jupyter Notebook
1
star