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    44 repositories

    • mhcflurry

      Public
      Peptide-MHC I binding affinity prediction
      Python
      •
      Apache License 2.0
      •57•191•7•0•Updated Sep 25, 2024Sep 25, 2024

    • gene-lists

      Public
      Gene lists related to cancer immunotherapy
      Jupyter Notebook
      •
      Apache License 2.0
      •3•13•1•0•Updated Sep 11, 2024Sep 11, 2024

    • varlens

      Public
      commandline manipulation of genomic variants and NGS reads
      Python
      •
      Apache License 2.0
      •2•19•6•0•Updated Sep 6, 2024Sep 6, 2024

    • vaxrank

      Public
      Ranked vaccine peptides for personalized cancer immunotherapy
      Python
      •
      Apache License 2.0
      •21•53•44•2•Updated Aug 8, 2024Aug 8, 2024

    • neoantigen-vaccine-pipeline

      Public
      Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines
      Python
      •
      Apache License 2.0
      •25•75•48•2•Updated Aug 7, 2024Aug 7, 2024

    • mhctools

      Public
      Python interface to running command-line and web-based MHC binding predictors
      Python
      •
      Apache License 2.0
      •21•89•17•0•Updated Jul 18, 2024Jul 18, 2024

    • varcode

      Public
      Library for manipulating genomic variants and predicting their effects
      Python
      •
      Apache License 2.0
      •25•81•33•0•Updated Jul 3, 2024Jul 3, 2024

    • pepdata

      Public
      Python interface to amino acid properties and IEDB
      Python
      •
      Apache License 2.0
      •17•49•5•1•Updated Jun 11, 2024Jun 11, 2024

    • pyensembl

      Public
      Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
      Python
      •
      Apache License 2.0
      •65•374•67•3•Updated Jun 4, 2024Jun 4, 2024

    • gtfparse

      Public
      Parsing tools for GTF (gene transfer format) files
      Python
      •
      Apache License 2.0
      •25•109•15•1•Updated Apr 12, 2024Apr 12, 2024

    • serializable

      Public
      Base class with serialization methods for user-defined Python objects
      Python
      •
      Apache License 2.0
      •3•0•2•1•Updated Apr 5, 2024Apr 5, 2024

    • sercol

      Public
      Serializable collection class with filtering and grouping methods
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 14, 2024Feb 14, 2024

    • isovar

      Public
      Assembly of RNA reads to determine the effect of a cancer mutation on protein sequence
      Python
      •
      Apache License 2.0
      •13•25•34•0•Updated Feb 13, 2024Feb 13, 2024

    • datacache

      Public
      Helpers for transparently downloading datasets
      Python
      •
      Apache License 2.0
      •7•5•7•0•Updated Feb 13, 2024Feb 13, 2024

    • ensembl-data

      Public
      Mirror of GTF and FASTA data from the Ensembl FTP servers
      1•0•0•1•Updated Feb 12, 2024Feb 12, 2024

    • mhcflurry-web

      Public
      Webapp for MHCflurry predictor
      CSS
      •
      Apache License 2.0
      •2•2•7•2•Updated Oct 26, 2023Oct 26, 2023

    • proteopt

      Public
      Common interface to protein design tools and structure predictors
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Jun 26, 2023Jun 26, 2023

    • mhcnames

      Public
      All the fun and adventure of MHC naming, now in Python
      Python
      •
      Apache License 2.0
      •4•9•9•0•Updated Dec 2, 2022Dec 2, 2022

    • mhc2flurry

      Public
      MHC class II binding predictor, under development
      Jupyter Notebook
      •
      Apache License 2.0
      •1•1•0•0•Updated Apr 26, 2021Apr 26, 2021

    • phipkit

      Public
      PhIP-seq data analysis workflow
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 6, 2021Mar 6, 2021

    • cov-2-mutations-by-lineage

      Public
      Quick analysis to associate SARS-Cov-2 spike mutations with pangolin lineages using GISAID data
      Jupyter Notebook
      •
      Apache License 2.0
      •0•1•1•0•Updated Mar 2, 2021Mar 2, 2021

    • files

      Public
      Reference genomes and related files used across repos and analyses
      0•0•0•0•Updated Oct 27, 2020Oct 27, 2020

    • mhcflurry-motifs

      Public
      Motifs for MHC I alleles as predicted by MHCflurry
      Python
      •
      Apache License 2.0
      •2•1•1•0•Updated Jul 30, 2020Jul 30, 2020

    • coronavirus-sequences

      Public
      Apache License 2.0
      •0•0•0•0•Updated Apr 3, 2020Apr 3, 2020

    • sarscov2-primers

      Public
      Genome amplification primers for SARS-CoV2 from ARTIC v1 with modification to 2019_76_RIGHT
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 16, 2020Mar 16, 2020

    • sarscov2-brazil-seqdata

      Public
      Exploring the sequencing data from SARSCoV2 patient SPBR1 in Brazil
      Shell
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 15, 2020Mar 15, 2020

    • openvax.github.io

      Public
      openvax.github.io
      JavaScript
      •0•0•0•0•Updated Feb 19, 2020Feb 19, 2020

    • hla-e-ligands

      Public
      List of published peptide ligands for HLA-E
      Apache License 2.0
      •0•0•0•0•Updated Aug 21, 2019Aug 21, 2019

    • synoptiko

      Public
      Summary report of somatic mutations from cancer DNA sequencing data
      Python
      •
      Apache License 2.0
      •0•0•17•0•Updated Aug 13, 2019Aug 13, 2019

    • vafster

      Public
      Extract allelic fractions from all the horrible ways VCFs encode allele counts
      Apache License 2.0
      •0•0•0•0•Updated Jun 20, 2019Jun 20, 2019