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    31 repositories

    • starcall-workflow

      Public
      A snakemake pipeline for the processing of in situ sequencing data. Provides improvements to stitching, alignment, and read calling all in a scalable and memory…
      Python
      •
      MIT License
      •0•1•0•0•Updated Jan 22, 2026Jan 22, 2026

    • constitch

      Public
      A python MIST inspired microscopy stitching library created to provide accurate stitching across many imaging cycles, with additional features such as differing…
      Python
      •
      MIT License
      •0•1•0•0•Updated Dec 12, 2025Dec 12, 2025

    • starcall

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Dec 12, 2025Dec 12, 2025

    • starcall-docs

      Public
      Python
      •0•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • MAVEable-Genes

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Sep 30, 2025Sep 30, 2025

    • bcl2fastqpear

      Public
      scripts and instructions for demultiplexing Illumina runs on the GS cluster
      Shell
      •0•0•0•0•Updated Sep 3, 2025Sep 3, 2025

    • Split_set_copy

      Public
      Replacement for NEB Split set GGA tool
      Jupyter Notebook
      •1•0•0•0•Updated Aug 24, 2025Aug 24, 2025

    • visseq

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jul 6, 2025Jul 6, 2025

    • fisseqtools

      Public
      Python
      •1•1•0•0•Updated Jun 25, 2025Jun 25, 2025

    • NRG_MAVEs_in_clinic

      Public
      Multiplexed assays of variant effect for clinical variant interpretation
      0•1•0•0•Updated Mar 20, 2025Mar 20, 2025

    • pacybara

      Public
      A pacbio barcode clustering and barseq pipeline that functions on the UWGS cluster
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 17, 2025Mar 17, 2025

    • clusterUtil

      Public
      utility scripts for HPC cluster usage
      Shell
      •3•0•0•0•Updated Mar 17, 2025Mar 17, 2025

    • Enrich2

      Public
      Tool for deep mutational scanning experiments.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •19•57•20•1•Updated Mar 11, 2025Mar 11, 2025

    • PIPEseq

      Public
      Python
      •0•0•0•0•Updated Mar 6, 2025Mar 6, 2025

    • 2024_multistep

      Public
      Data and analysis for MultiSTEP project
      Shell
      •0•0•0•0•Updated Jan 21, 2025Jan 21, 2025

    • Enrich2-Example

      Public
      Example deep mutational scanning dataset for Enrich2
      Creative Commons Attribution Share Alike 4.0 International
      •0•8•1•0•Updated Jan 17, 2025Jan 17, 2025

    • 2024_CSR_TFO

      Public
      Python
      •0•0•0•0•Updated Oct 31, 2024Oct 31, 2024

    • cyp2c19_2c9

      Public
      Analysis pipeline for "Understanding the CYP family tree through deep mutational scanning: A joint analysis of CYP2C19 and 2C9 variant abundance"
      1•1•0•0•Updated Sep 3, 2024Sep 3, 2024

    • VEP-calibrations

      Public
      Python
      •0•1•0•0•Updated Jun 7, 2024Jun 7, 2024

    • 2022_SrcHsp90

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 22, 2022Nov 22, 2022

    • simdms

      Public
      Deep mutational scanning dataset simulator.
      Python
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Sep 23, 2021Sep 23, 2021

    • 2020_dOTS

      Public
      Sequencing and statistical analysis for Rose, J.C., Popp, N.A., et al. 2020. Suppression of unwanted CRISPR/Cas9 editing by co-administration of catalytically i…
      Python
      •0•0•0•1•Updated Mar 25, 2021Mar 25, 2021

    • 2020_CAVA

      Public
      Data and analyses associated with CAVA
      0•0•0•0•Updated Oct 27, 2020Oct 27, 2020

    • VKOR

      Public
      Analysis pipeline for manuscript "Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact."
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Aug 31, 2020Aug 31, 2020

    • vcs_2019

      Public
      Code and processed data for manuscript entitled, "High-throughput, Microscope-based Sorting to Dissect Cellular Heterogeneity"
      Jupyter Notebook
      •1•1•0•0•Updated May 25, 2020May 25, 2020

    • amyloidBeta2019

      Public
      Analysis of amyloid ß large scale mutagenesis data by Gray et al. 2019
      0•0•0•0•Updated Oct 20, 2019Oct 20, 2019

    • LentiLandingPad

      Public
      HTML
      •0•0•0•0•Updated Aug 14, 2019Aug 14, 2019

    • 2019_SrcActivity

      Public
      Data and code for Ahler et al 2019
      0•1•0•0•Updated Apr 5, 2019Apr 5, 2019

    • VAMPseq

      Public
      We developed Variant Abundance by Massively Parallel Sequencing (VAMP-seq), which simultaneously measures the effects of thousands of missense variants on prote…
      HTML
      •3•5•0•0•Updated May 19, 2018May 19, 2018

    • Envision2017

      Public
      We present Envision, an accurate predictor of protein variant molecular effect, trained using large-scale experimental mutagenesis data. All data and software i…
      machine-learningenvision2017variant-effect-prediction
      Jupyter Notebook
      •1•19•0•0•Updated Jan 5, 2018Jan 5, 2018