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/
Mainz, Germany
Pinned Repositories
covigator
CoVigator - Monitoring SARS-CoV-2 mutations
covigator-ngs-pipeline
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.
EasyFuse
EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
neofox
Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors
seq2HLA
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.
splice2neo
R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes
TCLP
an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression
tronflow-alignment
Nextflow pipeline for BWA, BWA2 and STAR alignments
tronflow-mutect2
Nextflow pipeline for Mutect2 somatic variant calling best practices
vafator
Annotate variants in a VCF file with technical annotations from one or more BAMs
Bioinformatics Group at TRON - Translational Oncology at the Medical Center of the Johannes Gutenberg-University Mainz gGmbH's Repositories
TRON-Bioinformatics/EasyFuse
EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
TRON-Bioinformatics/seq2HLA
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/neofox
Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors
TRON-Bioinformatics/tronflow-mutect2
Nextflow pipeline for Mutect2 somatic variant calling best practices
TRON-Bioinformatics/covigator-ngs-pipeline
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/splice2neo
R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes
TRON-Bioinformatics/tronflow-alignment
Nextflow pipeline for BWA, BWA2 and STAR alignments
TRON-Bioinformatics/covigator
CoVigator - Monitoring SARS-CoV-2 mutations
TRON-Bioinformatics/TCLP
an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression
TRON-Bioinformatics/tronflow-hla-hd
A Nextflow workflow for HLA typing using HLA-HD
TRON-Bioinformatics/tronflow-bam-preprocessing
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-vcf-postprocessing
A Nextflow variant normalization pipeline based on vt and bcftools
TRON-Bioinformatics/easyquant
Quantification of reads at defined positions to verify custom input sequences.
TRON-Bioinformatics/variantmedium
TRON-Bioinformatics/milneo_analysis
Code related to the manuscript "Multiple instance learning to predict immune checkpoint blockade efficacy using neoantigen candidates"
TRON-Bioinformatics/nf-core-modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
TRON-Bioinformatics/nf-core-test-datasets
Test data to be used for automated testing with the nf-core pipelines
TRON-Bioinformatics/splicing_manuscript_scripts
Scripts related to the manuscript "Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates"
TRON-Bioinformatics/tronflow
TronFlow documentation
TRON-Bioinformatics/tronflow-copy-number-calling
A nextflow workflow for copy number calling
TRON-Bioinformatics/tronflow-test-data
A collection of test data for our TronFlow pipelines
TRON-Bioinformatics/curahack
TRON-Bioinformatics/easyfuse-src
EasyFuse source code to build python package
TRON-Bioinformatics/bioconda-recipes
Conda recipes for the bioconda channel.
TRON-Bioinformatics/covigator-analysis
Some data analysis and prototypes from the CoVigator project
TRON-Bioinformatics/covigator-intrahost-model
TRON-Bioinformatics/env2sif
Python script for creating and editing Singularity images on a HPC servers without sudo rights.
TRON-Bioinformatics/mavis-bench
Merging, Annotation, Validation, and Illustration of Structural variants
TRON-Bioinformatics/nf-template
Nextflow template for fast pipeline generation
TRON-Bioinformatics/snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see