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    51 repositories

    • proteinpaint

      Public
      Data visualization and analysis framework focused on phenotype-molecular data integration at cohort level.
      JavaScript
      •
      Other
      •13•42•93•3•Updated Dec 15, 2025Dec 15, 2025

    • icore-image

      Public
      Python
      •
      Other
      •0•4•3•1•Updated Dec 10, 2025Dec 10, 2025

    • 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
      Perl
      •
      Other
      •22•41•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•23•0•0•Updated Nov 21, 2025Nov 21, 2025

    • ROSE

      Public
      ROSE: RANK ORDERING OF SUPER-ENHANCERS
      softwarechip
      Python
      •
      Other
      •16•58•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
      •0•1•1•1•Updated Jul 10, 2025Jul 10, 2025

    • LASER

      Public
      R
      •
      GNU General Public License v2.0
      •0•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
      •0•0•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•15•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
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 4, 2025Apr 4, 2025

    • fuzzion2

      Public
      fuzzy fusion finder
      HTML
      •
      Apache License 2.0
      •3•6•0•0•Updated Feb 14, 2025Feb 14, 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

    • learngenomics.dev

      Public
      A guided, intuitive introduction to genomics for software engineers. Curated by the community.
      JavaScript
      •
      Other
      •38•386•7•10•Updated Aug 25, 2024Aug 25, 2024

    • RNApeg

      Public
      RNA junction finder
      Perl
      •
      Apache License 2.0
      •2•3•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.
      bioinformaticsphasinggenotypingrealignmentindel
      C
      •
      Apache License 2.0
      •3•12•0•0•Updated Jan 22, 2024Jan 22, 2024

    • DeepMRIRec

      Public
      Deep learning based pipeline for MRI reconstruction
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Jan 8, 2024Jan 8, 2024

    • cosima

      Public
      Python
      •0•0•0•0•Updated Jan 5, 2024Jan 5, 2024

    • SVIndelGenotyper

      Public
      Analysis of error profiles of Indels and structural variants in deep sequencing data
      whole-genome-sequencingsequencing-errorindel-analysissv-analysis
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Aug 28, 2023Aug 28, 2023

    • punctatools

      Public
      Detection, colocalization, and quantification of spots / puncta
      Jupyter Notebook
      •
      Other
      •9•14•7•1•Updated Mar 22, 2023Mar 22, 2023