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    58 repositories

    • prescient

      Public
      Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
      Python
      •
      MIT License
      •6•43•0•0•Updated Jun 25, 2024Jun 25, 2024

    • counterselection

      Public
      counterselection
      Jupyter Notebook
      •0•0•0•0•Updated Jun 9, 2024Jun 9, 2024

    • spatzie

      Public
      Identification of enriched motif pairs from chromatin interaction data
      bioinformaticsr-packagehicchia-pethichip
      R
      •
      GNU General Public License v3.0
      •3•1•0•0•Updated Feb 4, 2024Feb 4, 2024

    • idr2d

      Public
      Irreproducible discovery rate for genomic interaction data
      R
      •
      Other
      •3•2•0•0•Updated Feb 3, 2024Feb 3, 2024

    • gifford-lab.github.io

      Public
      New group website.
      SCSS
      •
      MIT License
      •0•0•0•0•Updated Jan 11, 2024Jan 11, 2024

    • PIQ

      Public
      R
      •0•0•0•0•Updated Jan 10, 2024Jan 10, 2024

    • overinterpretation

      Public
      Code for Overinterpretation paper
      Jupyter Notebook
      •
      MIT License
      •7•19•1•3•Updated Jul 6, 2023Jul 6, 2023

    • DiminishingReturns

      Public
      Constrained Submodular Optimization
      Jupyter Notebook
      •1•1•0•0•Updated Apr 27, 2023Apr 27, 2023

    • MIT-T-COVID-vaccine

      Public
      Code for MIT-T-COVID vaccine paper
      Jupyter Notebook
      •1•1•0•0•Updated Mar 31, 2023Mar 31, 2023

    • mit-6.S977

      Public
      HTML
      •1•0•0•0•Updated May 3, 2022May 3, 2022

    • FactorizableLibrary

      Public
      Code and data for factorizable libraries
      Jupyter Notebook
      •1•3•0•0•Updated Apr 8, 2022Apr 8, 2022

    • DeepLigand

      Public
      Python
      •
      MIT License
      •12•17•8•0•Updated Mar 22, 2022Mar 22, 2022

    • PUFFIN

      Public
      Python
      •
      MIT License
      •6•17•5•0•Updated Mar 20, 2022Mar 20, 2022

    • ReprogrammingRecovery

      Public
      Code for creating consensus motif database and performing motif enrichment
      Python
      •
      Other
      •3•6•0•0•Updated Feb 20, 2022Feb 20, 2022

    • mit-6.881

      Public
      HTML
      •0•0•0•0•Updated Jan 27, 2022Jan 27, 2022

    • seqgra

      Public
      seqgra: Synthetic rule-based biological sequence data generation for architecture evaluation and search
      Python
      •
      MIT License
      •2•2•0•0•Updated Jan 17, 2022Jan 17, 2022

    • optivax

      Public
      OpenEdge ABL
      •
      MIT License
      •8•22•1•0•Updated Dec 20, 2021Dec 20, 2021

    • deepaccess-package

      Public
      Methods for training and interpretation of an ensemble of neural networks for multi-task functional prediction of accessibility or histone modifications from DNA sequence.
      deep-learninggenomicsbiocondaepigenomicspypi-packageinterpretation
      Python
      •
      MIT License
      •0•5•0•0•Updated Sep 26, 2021Sep 26, 2021

    • motor-neuron-maturation

      Public
      Supporting code for motor neuron maturation manuscript
      Python
      •1•0•0•0•Updated Apr 9, 2021Apr 9, 2021

    • skipguide-analysis

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 31, 2021Mar 31, 2021

    • skipguide

      Public
      Predictive model for CRISPR-Cas9 mediated Exon Skipping
      Python
      •
      MIT License
      •0•3•0•0•Updated Mar 31, 2021Mar 31, 2021

    • MHC2-optimization

      Public
      Jupyter Notebook
      •2•1•0•0•Updated Mar 21, 2021Mar 21, 2021

    • High-Resolution-STARRseq

      Public
      Starrseq Analysis with the Sherwood Lab
      Jupyter Notebook
      •0•0•0•0•Updated Oct 26, 2020Oct 26, 2020

    • prescient-analysis

      Public
      Notebooks for pre-processing, analysis, and visualization of PRESCIENT applied to in vitro hematopoeisis (Weinreb et al. 2020) and in vitro beta-cell differentiation (Veres et al. 2019).
      Jupyter Notebook
      •4•4•2•0•Updated Oct 21, 2020Oct 21, 2020

    • MIAA-analysis

      Public
      Jupyter Notebook
      •2•0•0•0•Updated Aug 9, 2020Aug 9, 2020

    • DeepAccess

      Public
      Code for training, testing, and motif extraction from multilabel DNA sequence ensemble of convolutional neural networks
      Python
      •
      MIT License
      •3•1•0•0•Updated Aug 9, 2020Aug 9, 2020

    • antibody-2019

      Public
      Python
      •13•32•3•0•Updated Jul 22, 2020Jul 22, 2020

    • mit-6884.github.io

      Public
      Computational Aspects of Therapeutic Design
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Nov 8, 2019Nov 8, 2019

    • 6884-antibodies-data

      Public
      Problem Set 2 Data
      0•1•0•0•Updated Oct 25, 2019Oct 25, 2019

    • disentangled

      Public
      Python
      •0•0•0•0•Updated Oct 2, 2019Oct 2, 2019