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@TRON-Bioinformatics

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

TRON is a biopharmaceutical research organization dedicated to translational research in the field of oncology. Imprint: http://tron-mainz.de/imprint/

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  1. EasyFuse EasyFuse Public

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

    Python 49 13

  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 46 7

  3. neofox neofox Public

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

    Python 26 6

  4. tronflow-mutect2 tronflow-mutect2 Public

    Nextflow pipeline for Mutect2 somatic variant calling best practices

    Nextflow 20 3

  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 17 7

  6. splice2neo splice2neo Public

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

    R 13 1

Repositories

Showing 10 of 40 repositories
  • easyquant Public

    Quantification of reads at defined positions to verify custom input sequences.

    TRON-Bioinformatics/easyquant’s past year of commit activity
    Python 3 MIT 0 2 0 Updated Sep 19, 2024
  • 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 0 184 0 0 Updated Sep 13, 2024
  • 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 49 GPL-3.0 13 13 1 Updated Aug 26, 2024
  • covigator Public

    CoVigator - Monitoring SARS-CoV-2 mutations

    TRON-Bioinformatics/covigator’s past year of commit activity
    Python 11 MIT 1 6 3 Updated Aug 2, 2024
  • bioconda-recipes Public Forked from bioconda/bioconda-recipes

    Conda recipes for the bioconda channel.

    TRON-Bioinformatics/bioconda-recipes’s past year of commit activity
    Shell 0 MIT 3,230 0 0 Updated Aug 1, 2024
  • neofox Public

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

    TRON-Bioinformatics/neofox’s past year of commit activity
    Python 26 GPL-3.0 6 4 0 Updated Jul 31, 2024
  • 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 13 1 1 0 Updated Jul 23, 2024
  • tronflow-alignment Public

    Nextflow pipeline for BWA, BWA2 and STAR alignments

    TRON-Bioinformatics/tronflow-alignment’s past year of commit activity
    Nextflow 12 MIT 3 0 1 Updated Jul 22, 2024
  • 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.

    TRON-Bioinformatics/covigator-ngs-pipeline’s past year of commit activity
    Nextflow 17 MIT 7 5 2 Updated Jul 11, 2024
  • tronflow-bam-preprocessing Public

    Nextflow pipeline for the preprocessing of BAM files based on GATK best practices. Marking duplicates, realignment around indels, base quality score recalibration (BQSR) and reporting of metrics are optional to maintain flexibility for different use cases.

    TRON-Bioinformatics/tronflow-bam-preprocessing’s past year of commit activity
    Nextflow 5 MIT 0 4 1 Updated Jul 4, 2024
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