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    24 repositories

    • FinaleToolkit

      Public
      FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.
      bioinformaticsgenomicscomputational-biologycfdnaepigenomicscell-free-dnabioinformatics-toolfragmentomicsgenomics-analysis
      Python
      •
      MIT License
      •10•26•3•0•Updated Jul 1, 2025Jul 1, 2025

    • finaledb_workflow

      Public
      Python
      •
      MIT License
      •2•4•1•0•Updated Jun 24, 2025Jun 24, 2025

    • FinaleMe_workflow

      Public
      Run FinaleMe methylation prediction and tissue-of-origin analysis on several BAM files
      R
      •
      MIT License
      •0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

    • finaletoolkit_workflow

      Public
      Extract Finaletoolkit features from several files
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 2, 2025Jun 2, 2025

    • FinaleMe

      Public
      Java
      •
      MIT License
      •3•14•4•1•Updated May 23, 2025May 23, 2025

    • CRAGR_v2

      Public
      CRAGR_v2 is a CRAGR pipeline that handles hotspots calling for multiple replicates using the irreproducible discovery rate (IDR).
      R
      •
      MIT License
      •0•2•0•0•Updated Mar 18, 2025Mar 18, 2025

    • bedtorch

      Public
      Fast and native toolsuite for BED file manipulation
      HTML
      •
      Other
      •5•0•0•0•Updated Feb 27, 2025Feb 27, 2025

    • cragr

      Public
      R package for CRAG
      R
      •
      Other
      •4•11•0•1•Updated Feb 17, 2025Feb 17, 2025

    • MethylSeqDesign

      Public
      MethylSeqDesign is a framework for power calculation and study design of Methy-Seq experiments by utilizing information from pilot data.
      R
      •1•0•0•0•Updated Feb 11, 2025Feb 11, 2025

    • POWEREDBiSeq

      Public
      Scripts for POWEREDBiSeq, a tool which estimates power in bisulfite sequencing studies
      R
      •1•0•0•0•Updated Feb 10, 2025Feb 10, 2025

    • finaletoolkit-docs

      Public
      HTML
      •0•0•0•0•Updated Oct 10, 2024Oct 10, 2024

    • epifluidlab.github.io

      Public
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•3•Updated Sep 5, 2024Sep 5, 2024

    • wf-pore-c

      Public
      Nextflow
      •
      Other
      •11•0•0•0•Updated May 29, 2024May 29, 2024

    • MAGNIFIER

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 15, 2024Mar 15, 2024

    • FRAGMA

      Public
      A recreation of the FRAGmentomics-based Methylation Analysis (FRAGMA) from Zhou et al. 2022
      Jupyter Notebook
      •
      Apache License 2.0
      •1•0•0•0•Updated Jan 17, 2024Jan 17, 2024

    • finaledb_portal

      Public
      JavaScript
      •
      MIT License
      •1•3•0•0•Updated Jan 3, 2024Jan 3, 2024

    • hictools

      Public
      Simple home-made tools for Hi-C analysis
      R
      •
      Other
      •1•0•0•0•Updated Jun 27, 2022Jun 27, 2022

    • pairix

      Public
      1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
      C
      •
      MIT License
      •15•0•0•0•Updated Nov 20, 2021Nov 20, 2021

    • juicer4snakemake

      Public
      Juicer pipeline re-implemented with Snakemake
      Shell
      •
      MIT License
      •0•0•0•0•Updated Aug 30, 2021Aug 30, 2021

    • CRAG

      Public
      De novo characterization of cell-free DNA fragmentation hotspots
      MATLAB
      •
      MIT License
      •2•5•0•0•Updated Aug 21, 2021Aug 21, 2021

    • juicer

      Public
      A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
      Shell
      •
      MIT License
      •189•0•0•0•Updated Aug 19, 2021Aug 19, 2021

    • Rhtslib12

      Public
      HTSlib high-throughput sequencing library as an R package
      C
      •13•0•0•0•Updated Apr 13, 2021Apr 13, 2021

    • bedr

      Public
      ❗ This is a read-only mirror of the CRAN R package repository. bedr — Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'
      R
      •4•0•0•0•Updated Mar 19, 2021Mar 19, 2021

    • DoGFinder

      Public
      Python
      •11•0•0•0•Updated Nov 5, 2020Nov 5, 2020