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    45 repositories

    • proteinpaint

      Public
      Data visualization and analysis framework focused on phenotype-molecular data integration at cohort level.
      JavaScript
      •
      Other
      •5•22•84•3•Updated Jan 2, 2025Jan 2, 2025

    • RNAIndel

      Public
      Somatic indel discovery tool for tumor RNA-Seq data.
      Python
      •
      Apache License 2.0
      •9•21•0•1•Updated Jan 2, 2025Jan 2, 2025

    • seaseq

      Public
      Abraham's lab - ChipSeq Pipeline
      WDL
      •
      Apache License 2.0
      •5•6•0•0•Updated Dec 2, 2024Dec 2, 2024

    • XenoCP

      Public
      A cloud-based tool for mouse read cleansing in xenograft samples
      Shell
      •
      Apache License 2.0
      •3•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
      •32•352•7•3•Updated Aug 25, 2024Aug 25, 2024

    • RNApeg

      Public
      RNA junction finder
      Perl
      •
      Apache License 2.0
      •2•3•1•0•Updated Aug 22, 2024Aug 22, 2024

    • BOUQUET

      Public
      R
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Aug 14, 2024Aug 14, 2024

    • ROSE

      Public
      ROSE: RANK ORDERING OF SUPER-ENHANCERS
      softwarechip
      Python
      •
      Other
      •12•43•2•0•Updated Aug 2, 2024Aug 2, 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

    • CICERO

      Public
      CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
      cicerofusion-detectionrna-seq
      Perl
      •
      Other
      •19•35•8•0•Updated Jan 24, 2024Jan 24, 2024

    • indelPost

      Public
      Python library for simple and complex indels.
      phasinggenotypingrealignmentindelbioinformatics
      C
      •
      Apache License 2.0
      •3•13•0•0•Updated Jan 22, 2024Jan 22, 2024

    • DeepMRIRec

      Public
      Deep learning based pipeline for MRI reconstruction
      Jupyter Notebook
      •
      MIT License
      •2•0•0•1•Updated Jan 8, 2024Jan 8, 2024

    • cosima

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

    • Dowen_Fan

      Public
      Abraham lab ChIA-PET analysis pipeline
      Shell
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Dec 20, 2023Dec 20, 2023

    • WARDEN

      Public
      Source code for the WARDEN DNAnexus apps
      Python
      •0•1•0•0•Updated Nov 20, 2023Nov 20, 2023

    • 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

    • SICER2

      Public
      sicer2
      Python
      •
      MIT License
      •1•0•1•0•Updated Aug 21, 2023Aug 21, 2023

    • fuzzion2

      Public
      fuzzy fusion finder
      C++
      •
      Apache License 2.0
      •2•6•0•0•Updated Aug 7, 2023Aug 7, 2023

    • punctatools

      Public
      Detection, colocalization, and quantification of spots / puncta
      Jupyter Notebook
      •
      Other
      •7•12•7•1•Updated Mar 22, 2023Mar 22, 2023

    • TALL-example

      Public
      R
      •0•2•0•0•Updated Mar 15, 2023Mar 15, 2023

    • 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 Jan 18, 2023Jan 18, 2023

    • PrimerTK

      Public
      A toolkit to design standard primers, multiplexed primers, and primers around SV's
      Python
      •
      Apache License 2.0
      •4•12•5•1•Updated Oct 29, 2022Oct 29, 2022

    • teltale

      Public
      Compute telomeric read fractions in a BAM file.
      next-generation-sequencingbamtelomeres
      C++
      •
      Apache License 2.0
      •1•3•0•0•Updated Aug 23, 2022Aug 23, 2022

    • BAM2GFF

      Public
      BAMtoGFF, matrix density, plot visualizations
      Python
      •
      Other
      •47•4•0•0•Updated Jun 30, 2022Jun 30, 2022

    • am_utils

      Public
      Some useful functions
      Python
      •
      Other
      •1•0•0•0•Updated May 11, 2022May 11, 2022

    • ChIPseqSpikeInFree

      Public
      A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications
      R
      •
      Apache License 2.0
      •13•31•8•1•Updated Feb 22, 2022Feb 22, 2022

    • intake_io

      Public
      Image-focused IO for Python using intake and xarray
      Python
      •
      MIT License
      •2•0•0•0•Updated Jan 27, 2022Jan 27, 2022