TRON Bioinformatics

All

47 repositories

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.
Python
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MIT License
•9•49•15•2•Updated Jul 28, 2025Jul 28, 2025
VariantMedium
Public
Sensitive and generalizable somatic point mutation calling with 3D DenseNets
Python
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Other
•1•1•0•0•Updated Jul 15, 2025Jul 15, 2025
tronmake-modules
Public
A set of well defined SnakeMake modules for integration into pipelines.
MIT License
•0•0•0•0•Updated Jun 25, 2025Jun 25, 2025
snakemake-wrappers
Public
This is the development home of the Snakemake wrapper repository, see
Python
•195•0•0•0•Updated Jun 25, 2025Jun 25, 2025
arcasHLA
Public
Fast and accurate in silico inference of HLA genotypes from RNA-seq
Python
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GNU General Public License v3.0
•57•0•0•0•Updated Jun 23, 2025Jun 23, 2025
bioconda-recipes
Public
Conda recipes for the bioconda channel.
Shell
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MIT License
•3.6k•0•0•0•Updated Jun 5, 2025Jun 5, 2025
vafator
Public
Annotate variants in a VCF file with technical annotations from one or more BAMs
bioinformatics annotation vcf bam
Jupyter Notebook
•
MIT License
•0•9•10•0•Updated Jun 2, 2025Jun 2, 2025
bam2tensor
Public
Toolbox for generating tensors from BAM files
Python
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MIT License
•0•0•0•0•Updated Apr 23, 2025Apr 23, 2025
splice2neo
Public
R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes
R
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Other
•2•14•0•0•Updated Apr 15, 2025Apr 15, 2025
neofox
Public
Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors
immunogenomics immunogenicity-prediction cancer-immunology netmhciipan netmhcpan neoantigen-annotation neoantigens bioinformatics
Python
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GNU General Public License v3.0
•7•33•4•0•Updated Mar 18, 2025Mar 18, 2025
testp
Public
0•0•0•0•Updated Mar 14, 2025Mar 14, 2025
test
Public
Test project
0•0•0•0•Updated Mar 6, 2025Mar 6, 2025
easyquant
Public
Quantification of reads at defined positions to verify custom input sequences.
Python
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MIT License
•0•4•3•0•Updated Mar 5, 2025Mar 5, 2025
tronflow-strelka2
Public
Strelka2 nextflow pipeline
variant-calling bioinformatics genomics ngs
Nextflow
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MIT License
•0•1•0•0•Updated Feb 5, 2025Feb 5, 2025
nf-template
Public template
Nextflow template for fast pipeline generation
Nextflow
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GNU General Public License v3.0
•2•0•0•0•Updated Jan 28, 2025Jan 28, 2025
tronflow-haplotype-caller
Public
A nextflow pipeline implementing GATK's HaplotypeCaller best practices
nextflow gatk tronflow bioinformatics ngs
Nextflow
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MIT License
•0•1•2•0•Updated Jan 28, 2025Jan 28, 2025
tronflow-vcf-postprocessing
Public
A Nextflow variant normalization pipeline based on vt and bcftools
bioinformatics nextflow vt bcftools normalizing-variants tronflow vcf
Shell
•
MIT License
•1•6•1•0•Updated Jan 23, 2025Jan 23, 2025
EasyFuse
Public
EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
Python
•
GNU General Public License v3.0
•14•60•5•0•Updated Dec 12, 2024Dec 12, 2024
mavis-bench
Public
Merging, Annotation, Validation, and Illustration of Structural variants
Python
•
GNU General Public License v3.0
•14•0•0•0•Updated Oct 1, 2024Oct 1, 2024
covigator
Public
CoVigator - Monitoring SARS-CoV-2 mutations
dashboard dash coronavirus covid-19 sars-cov-2 bioinformatics
Python
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MIT License
•1•11•6•3•Updated Aug 2, 2024Aug 2, 2024
tronflow-alignment
Public
Nextflow pipeline for BWA, BWA2 and STAR alignments
bwa tronflow bioinformatics rna-seq ngs
Nextflow
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MIT License
•3•12•0•1•Updated Jul 22, 2024Jul 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.
nextflow variant-callers coronavirus covid-19 sars-cov-2 bioinformatics genomics ngs
Nextflow
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MIT License
•8•19•5•2•Updated Jul 11, 2024Jul 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.
picard bioinformatics nextflow gatk tronflow
Nextflow
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MIT License
•0•5•4•1•Updated Jul 4, 2024Jul 4, 2024
tronflow-hla-hd
Public
A Nextflow workflow for HLA typing using HLA-HD
hla-typing bioinformatics
Nextflow
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MIT License
•2•11•2•0•Updated Jul 3, 2024Jul 3, 2024
tronflow-mutect2
Public
Nextflow pipeline for Mutect2 somatic variant calling best practices
nextflow mutect2 tronflow bioinformatics
Nextflow
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MIT License
•4•22•2•2•Updated Jun 14, 2024Jun 14, 2024
tronflow-copy-number-calling
Public
A nextflow workflow for copy number calling
cnv bioinformatics
Nextflow
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MIT License
•0•1•0•1•Updated Jun 11, 2024Jun 11, 2024
curahack
Public
MIT License
•0•0•0•0•Updated Apr 25, 2024Apr 25, 2024
env2sif
Public
Python script for creating and editing Singularity images on a HPC servers without sudo rights.
Python
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Other
•0•1•2•0•Updated Apr 11, 2024Apr 11, 2024
splicing_manuscript_scripts
Public
Scripts related to the manuscript "Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates"
Shell
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MIT License
•0•1•0•0•Updated Mar 21, 2024Mar 21, 2024
TCLP
Public
an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression
0•10•2•0•Updated Feb 26, 2024Feb 26, 2024