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    17 repositories

    • Enrich2

      Public
      Tool for deep mutational scanning experiments.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •13•46•21•0•Updated Dec 7, 2024Dec 7, 2024

    • 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•0•0•0•Updated Sep 3, 2024Sep 3, 2024

    • VEP-calibrations

      Public
      Python
      •0•0•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•3•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 inactivating truncated guide RNAs. Nat. Comm.
      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 protein intracellular abundance, and applied it to study PTEN and TPMT, two clinically actionable genes. This repository houses the analysis scripts used for this study.
      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 in this study are freely available. The training data set and all code used to train the models and generate the figures presented in this manuscript are available here. Envision predictio…
      machine-learningenvision2017variant-effect-prediction
      Jupyter Notebook
      •1•17•0•0•Updated Jan 5, 2018Jan 5, 2018

    • 2017_GRAY_InformativeAA

      Public
      To draw general conclusions about the effects of different amino acid substitutions, we analyzed 34,373 mutations in fourteen proteins whose effects were measured using large-scale mutagenesis approaches. Methionine was the most tolerated substitution while proline was the least tolerated. Histidine and asparagine best recapitulated the effects …
      1•1•0•0•Updated Jul 28, 2017Jul 28, 2017

    • Enrich2-Example

      Public
      Example deep mutational scanning dataset for Enrich2
      Creative Commons Attribution Share Alike 4.0 International
      •0•5•1•0•Updated Sep 17, 2016Sep 17, 2016