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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 46 12

  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 44 7

  3. neofox neofox Public

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

    Python 25 5

  4. tronflow-mutect2 tronflow-mutect2 Public

    Nextflow pipeline for Mutect2 somatic variant calling best practices

    Nextflow 19 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 39 repositories
  • 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
  • neofox Public

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

    TRON-Bioinformatics/neofox’s past year of commit activity
    Python 25 GPL-3.0 5 4 0 Updated Jul 11, 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 11, 2024
  • 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 Jul 9, 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
  • tronflow-hla-hd Public

    A Nextflow workflow for HLA typing using HLA-HD

    TRON-Bioinformatics/tronflow-hla-hd’s past year of commit activity
    Nextflow 5 MIT 0 0 0 Updated Jul 3, 2024
  • tronflow-vcf-postprocessing Public

    A Nextflow variant normalization pipeline based on vt and bcftools

    TRON-Bioinformatics/tronflow-vcf-postprocessing’s past year of commit activity
    Shell 6 MIT 1 1 0 Updated Jul 1, 2024
  • tronflow-mutect2 Public

    Nextflow pipeline for Mutect2 somatic variant calling best practices

    TRON-Bioinformatics/tronflow-mutect2’s past year of commit activity
    Nextflow 19 MIT 3 2 2 Updated Jun 14, 2024
  • tronflow-copy-number-calling Public

    A nextflow workflow for copy number calling

    TRON-Bioinformatics/tronflow-copy-number-calling’s past year of commit activity
    Nextflow 1 MIT 0 0 1 Updated Jun 11, 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 3,152 0 0 Updated May 29, 2024

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