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    18 repositories

    • PMDS_2026

      Public
      Personlig Medicin Data Science kursus 2025
      R
      •0•0•0•0•Updated May 5, 2026May 5, 2026

    • lionheart

      Public
      LIONHEART detects cancer from whole genome sequenced plasma cell-free DNA.
      cancer-genomicswhole-genome-sequencingcfdna
      cancer-genomicswhole-genome-sequencingcfdnacancer-detectioncell-free-dnachromatin-accessibiityfragmentomics
      Python
      •
      MIT License
      •3•11•1•0•Updated Apr 29, 2026Apr 29, 2026

    • Mutation_Informed_Fragmentomics

      Public
      A mutation-informed fragmentomics exploration framework for cfDNA
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 13, 2026Feb 13, 2026

    • UMIseq_variant_calling

      Public
      Detect somatic SNVs from deep targeted UMI-seq cfDNA
      variant-callingcell-freeumi-seq
      variant-callingcell-freeumi-seq
      Python
      •
      MIT License
      •0•2•0•0•Updated Jan 27, 2026Jan 27, 2026

    • ctDNAmer

      Public
      Snakemake workflow and codebase for ctDNA detection with k-mers
      Python
      •0•1•0•0•Updated Jan 22, 2026Jan 22, 2026

    • batch-NMF

      Public
      pytorch implementation of NMF extentions that incorporate batch effects including Batch NMF (bNMF) and Sigmoid Filter NMF (sfNMF).
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 18, 2025Sep 18, 2025

    • ccb_pipeline

      Public
      Snakemake workflow and codebase for the ContextCountBooster package
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 28, 2025Jul 28, 2025

    • contextcountbooster

      Public
      Sequence context count modeling with weights using xgboost
      Python
      •0•0•0•0•Updated Jul 28, 2025Jul 28, 2025

    • BBQ

      Public
      A somatic SNV variant caller that uses discordant overlapping read pairs to calculate sample-specific base error rates.
      Python
      •
      MIT License
      •0•2•0•0•Updated Feb 28, 2025Feb 28, 2025

    • bbq_pipeline

      Public
      Snakemake workflow for the Better Base Quality (BBQ) tool
      Python
      •
      MIT License
      •0•0•0•1•Updated Feb 28, 2025Feb 28, 2025

    • kmerPaPa

      Public
      Tool to calculate a "k-mer pattern partition" from position specific k-mer counts.
      bioinformaticsgenomicsgenomic-data-science
      bioinformaticsgenomicsgenomic-data-science
      Python
      •
      MIT License
      •0•2•0•0•Updated Jan 25, 2025Jan 25, 2025

    • genovo

      Public
      GeNovo - Identifying disease genes with de-novo mutations
      Rust
      •
      MIT License
      •1•0•0•0•Updated Nov 25, 2024Nov 25, 2024

    • kmer_counter

      Public
      Count k-mers in regions or at SNVs or at indel breakpoints.
      bioinformaticsgenomics
      bioinformaticsgenomics
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 27, 2024Aug 27, 2024

    • ctDNAtool

      Public
      A software for creating and manipulating statistics from cfDNA data
      Python
      •2•0•0•0•Updated Feb 11, 2024Feb 11, 2024

    • mutexpect

      Public
      Rust
      •
      MIT License
      •1•0•0•0•Updated Feb 9, 2023Feb 9, 2023

    • ROC-utils

      Public
      Python
      •0•0•0•0•Updated Dec 9, 2022Dec 9, 2022

    • Genovo_Input

      Public
      0•0•0•0•Updated Jan 17, 2022Jan 17, 2022

    • pattern_partition_prediction

      Public
      Rust
      •
      MIT License
      •1•0•0•0•Updated Oct 3, 2021Oct 3, 2021
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