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@TRON-Bioinformatics

TRON Bioinformatics

TRON - Translational Oncology at the Medical Center of the Johannes Gutenberg-University Mainz gGmbH

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  1. EasyFuse EasyFuse Public

    EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.

    Python 62 15

  2. seq2HLA seq2HLA Public

    In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA allel…

    Python 49 9

  3. neofox neofox Public

    Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors

    Python 33 7

  4. tronflow-mutect2 tronflow-mutect2 Public

    Nextflow pipeline for Mutect2 somatic variant calling best practices

    Nextflow 22 4

  5. covigator-ngs-pipeline covigator-ngs-pipeline Public

    A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, LoFreq and iVar.

    Nextflow 19 8

  6. splice2neo splice2neo Public

    R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes

    R 14 2

Repositories

Showing 10 of 52 repositories
  • splice2neo Public

    R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes

    TRON-Bioinformatics/splice2neo’s past year of commit activity
    R 14 2 0 0 Updated Oct 30, 2025
  • SpecHLA Public Forked from deepomicslab/SpecHLA

    SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data.

    TRON-Bioinformatics/SpecHLA’s past year of commit activity
    C++ 0 MIT 13 0 0 Updated Oct 15, 2025
  • mkGCPct Public Forked from soccin/mkGCPct

    Scripts to make GC% RDA files for FACETS

    TRON-Bioinformatics/mkGCPct’s past year of commit activity
    Shell 0 1 0 0 Updated Oct 14, 2025
  • EasyFuse Public

    EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.

    TRON-Bioinformatics/EasyFuse’s past year of commit activity
    Python 62 GPL-3.0 15 5 0 Updated Oct 10, 2025
  • mhcquant Public Forked from nf-core/mhcquant

    Identify and quantify MHC eluted peptides from mass spectrometry raw data

    TRON-Bioinformatics/mhcquant’s past year of commit activity
    Nextflow 0 MIT 32 0 0 Updated Sep 18, 2025
  • snakemake-wrappers Public Forked from snakemake/snakemake-wrappers

    This is the development home of the Snakemake wrapper repository, see

    TRON-Bioinformatics/snakemake-wrappers’s past year of commit activity
    Python 0 203 0 0 Updated Sep 17, 2025
  • DEEPctMUT Public

    Tumor-naïve ctDNA mutation detection pipeline

    TRON-Bioinformatics/DEEPctMUT’s past year of commit activity
    Python 1 MIT 0 2 0 Updated Sep 12, 2025
  • paneldesign Public

    R package to design and evaluate sequencing panels

    TRON-Bioinformatics/paneldesign’s past year of commit activity
    R 0 0 4 1 Updated Sep 7, 2025
  • vafator Public

    Annotate variants in a VCF file with technical annotations from one or more BAMs

    TRON-Bioinformatics/vafator’s past year of commit activity
    Jupyter Notebook 9 MIT 0 11 0 Updated Sep 1, 2025
  • seq2HLA Public

    In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.

    TRON-Bioinformatics/seq2HLA’s past year of commit activity
    Python 49 MIT 9 15 2 Updated Aug 9, 2025

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