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    53 repositories

    • proteinpaint

      Public
      Data visualization and analysis framework focused on phenotype-molecular data integration at cohort level.
      JavaScript
      •
      Other
      •14•48•94•6•Updated Apr 25, 2026Apr 25, 2026

    • fuzzion2

      Public
      fuzzy fusion finder
      HTML
      •
      Apache License 2.0
      •3•7•0•0•Updated Apr 22, 2026Apr 22, 2026

    • icore-image

      Public
      Python
      •
      Other
      •1•5•4•8•Updated Apr 17, 2026Apr 17, 2026

    • CSP

      Public
      validation and detection of heteroresistance in staphylococci and related features using cumulative survival profiling
      bayesianpapheteroresistance
      bayesianpapheteroresistancestaphylococci
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • zFISHer

      Public
      Python
      •
      MIT License
      •0•0•0•1•Updated Apr 13, 2026Apr 13, 2026

    • radial-intensity-analysis

      Public
      A snakemake workflow for performing radial intensity analysis of signals in the nucleolus
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Apr 7, 2026Apr 7, 2026

    • SVIndelGenotyper

      Public
      Analysis of error profiles of Indels and structural variants in deep sequencing data
      whole-genome-sequencingsequencing-errorindel-analysis
      whole-genome-sequencingsequencing-errorindel-analysissv-analysis
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 4, 2026Apr 4, 2026

    • learngenomics.dev

      Public
      A guided, intuitive introduction to genomics for software engineers. Curated by the community.
      JavaScript
      •
      Other
      •39•394•7•4•Updated Feb 8, 2026Feb 8, 2026

    • EasyFiji

      Public
      Source code for easyfiji project (maintain by Aaron Taylor and Chen LI)
      Java
      •
      MIT License
      •0•0•0•1•Updated Dec 1, 2025Dec 1, 2025

    • CICERO

      Public
      CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
      rna-seqcicerofusion-detection
      rna-seqcicerofusion-detection
      Perl
      •
      Other
      •22•43•7•0•Updated Nov 28, 2025Nov 28, 2025

    • RNAIndel

      Public
      Somatic indel discovery tool for tumor RNA-Seq data.
      Python
      •
      Apache License 2.0
      •8•24•0•0•Updated Nov 21, 2025Nov 21, 2025

    • ROSE

      Public
      ROSE: RANK ORDERING OF SUPER-ENHANCERS
      softwarechip
      softwarechip
      Python
      •
      Other
      •18•68•3•0•Updated Nov 14, 2025Nov 14, 2025

    • SICER2

      Public
      sicer2
      Python
      •
      MIT License
      •2•0•3•0•Updated Nov 14, 2025Nov 14, 2025

    • fuzzion2_patgen

      Public
      tools for creating patterns for use with fuzzion2
      Perl
      •
      Apache License 2.0
      •1•0•0•0•Updated Nov 5, 2025Nov 5, 2025

    • Semisupervised_Learning

      Public
      Development of an approach using semisupervised learning and multinomial logistic regression to label methylation samples to boost
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 14, 2025Aug 14, 2025

    • HiLOW

      Public
      HiC Looping Organization Workflow
      WDL
      •1•1•1•1•Updated Jul 10, 2025Jul 10, 2025

    • LASER

      Public
      R
      •
      GNU General Public License v2.0
      •1•0•0•0•Updated Jul 1, 2025Jul 1, 2025

    • Dowen_Fan

      Public
      Abraham lab ChIA-PET analysis pipeline
      Shell
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jul 1, 2025Jul 1, 2025

    • BOUQUET

      Public
      R
      •
      GNU General Public License v2.0
      •1•2•0•0•Updated Jul 1, 2025Jul 1, 2025

    • WARDEN

      Public
      Source code for the WARDEN DNAnexus apps
      Python
      •1•1•0•0•Updated May 16, 2025May 16, 2025

    • cis-x

      Public
      Search for activating regulatory variants in the tumor genome
      Perl
      •
      Apache License 2.0
      •8•14•4•0•Updated Apr 11, 2025Apr 11, 2025

    • Retinal_Analysis_Vas

      Public
      Software and tools to perform Vasculature and DAPI analysis on mouse retina
      stjude-cbi
      stjude-cbi
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 4, 2025Apr 4, 2025

    • seaseq

      Public
      Abraham's lab - ChipSeq Pipeline
      WDL
      •
      Apache License 2.0
      •5•7•2•1•Updated Dec 2, 2024Dec 2, 2024

    • XenoCP

      Public
      A cloud-based tool for mouse read cleansing in xenograft samples
      Shell
      •
      Apache License 2.0
      •2•5•0•1•Updated Nov 1, 2024Nov 1, 2024

    • Mouse_Survival

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•1•0•Updated Sep 13, 2024Sep 13, 2024

    • RNApeg

      Public
      RNA junction finder
      Perl
      •
      Apache License 2.0
      •2•4•2•0•Updated Aug 22, 2024Aug 22, 2024

    • dab_detector

      Public
      Scripts and classes for DAB plaque detection
      MATLAB
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Apr 5, 2024Apr 5, 2024

    • DeepBrainIPP

      Public
      Automated Brain Structures Segmentation Framework
      Python
      •
      Apache License 2.0
      •3•7•0•1•Updated Mar 22, 2024Mar 22, 2024

    • doCNA

      Public
      Python
      •1•2•1•0•Updated Feb 27, 2024Feb 27, 2024

    • indelPost

      Public
      Python library for simple and complex indels.
      bioinformaticsphasinggenotyping
      bioinformaticsphasinggenotypingrealignmentindel
      C
      •
      Apache License 2.0
      •3•12•0•0•Updated Jan 22, 2024Jan 22, 2024
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