Repositories list

• lionheart

  Public
  LIONHEART is a method for detecting cancer from whole genome sequenced plasma cell-free DNA.

  cancer-genomicswhole-genome-sequencingcfdna+ 4cancer-detectioncell-free-dnachromatin-accessibiityfragmentomics

  Python

  •

  MIT License

  •1•4•1•0•Updated Mar 2, 2025Mar 2, 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•0•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

  Python

  •

  MIT License

  •0•1•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

• UMIseq_variant_calling

  Public
  Detect somatic SNVs from deep targeted UMI-seq cfDNA

  Python

  •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

• kmer_counter

  Public
  Count k-mers in regions or at SNVs or at indel breakpoints.

  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