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/pyensembl
Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
openvax/mhcflurry
Peptide-MHC I binding affinity prediction
openvax/gtfparse
Parsing tools for GTF (gene transfer format) files
openvax/mhctools
Python interface to running command-line and web-based MHC binding predictors
openvax/varcode
Library for manipulating genomic variants and predicting their effects
openvax/neoantigen-vaccine-pipeline
Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines
openvax/vaxrank
Ranked vaccine peptides for personalized cancer immunotherapy
openvax/pepdata
Python interface to amino acid properties and IEDB
openvax/isovar
Assembly of RNA reads to determine the effect of a cancer mutation on protein sequence
openvax/varlens
commandline manipulation of genomic variants and NGS reads
openvax/gene-lists
Gene lists related to cancer immunotherapy
openvax/mhcnames
All the fun and adventure of MHC naming, now in Python
openvax/datacache
Helpers for transparently downloading datasets
openvax/mhcflurry-web
Webapp for MHCflurry predictor
openvax/cov-2-mutations-by-lineage
Quick analysis to associate SARS-Cov-2 spike mutations with pangolin lineages using GISAID data
openvax/mhc2flurry
MHC class II binding predictor, under development
openvax/mhcflurry-motifs
Motifs for MHC I alleles as predicted by MHCflurry
openvax/proteopt
Common interface to protein design tools and structure predictors
openvax/phipkit
PhIP-seq data analysis workflow
openvax/coronavirus-sequences
openvax/ensembl-data
Mirror of GTF and FASTA data from the Ensembl FTP servers
openvax/files
Reference genomes and related files used across repos and analyses
openvax/hla-e-ligands
List of published peptide ligands for HLA-E
openvax/openvax.github.io
openvax.github.io
openvax/sarscov2-brazil-seqdata
Exploring the sequencing data from SARSCoV2 patient SPBR1 in Brazil
openvax/sarscov2-primers
Genome amplification primers for SARS-CoV2 from ARTIC v1 with modification to 2019_76_RIGHT
openvax/sercol
Serializable collection class with filtering and grouping methods
openvax/serializable
Base class with serialization methods for user-defined Python objects
openvax/synoptiko
Summary report of somatic mutations from cancer DNA sequencing data
openvax/vafster
Extract allelic fractions from all the horrible ways VCFs encode allele counts