Skip to content

@bioinformatics-group bioinformatics-group

Change the repository type filter

All

    Repositories list

    24 repositories

    • TooT-BERT_ICAT

      Public
      TooT-BERT-ICAT utilizes ProtBERT-BFD to predict and classify inorganic ion-specific transmembrane transporter proteins with high precision and accuracy.
      Python
      •1•0•0•0•Updated Mar 27, 2024Mar 27, 2024

    • tootsuite-website

      Public
      The public website for the tootsuite project
      HTML
      •
      MIT License
      •1•0•4•0•Updated Oct 31, 2023Oct 31, 2023

    • TooT-BERT-T

      Public
      Transmembrane Transport Protein Predictor Using ProtBERT-BFD and Logistic Regression
      Python
      •
      MIT License
      •2•0•0•1•Updated Aug 3, 2023Aug 3, 2023

    • TooT-BERT-SC

      Public
      Classifies transmembrane transporter proteins by substrate using a majority-vote approach with various standard predictors
      Python
      •1•0•0•0•Updated Jun 1, 2023Jun 1, 2023

    • TooT-Proteome

      Public
      A tool to combine Toot-T and Toot-SC to more quickly classify transporter proteins
      Python
      •
      MIT License
      •2•1•1•0•Updated Apr 5, 2023Apr 5, 2023

    • toot_bert_m

      Public
      Discriminating membrane proteins from non-membrane proteins using a BERT representation of protein primary sequences
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 4, 2023Apr 4, 2023

    • TooT-BERT-Proteome

      Public
      Predicts transmembrane transporter proteins and their substrate-specific properties using BERT-based predictors for transporter and substrate classification
      MIT License
      •0•0•0•0•Updated Mar 31, 2023Mar 31, 2023

    • bioinformatics-singularity

      Public
      The software we use to run things in our lab
      Singularity
      •
      MIT License
      •2•1•9•0•Updated May 6, 2022May 6, 2022

    • TooT-SC

      Public
      R
      •
      MIT License
      •3•2•3•0•Updated May 4, 2022May 4, 2022

    • TooT-T

      Public
      Tool to predict transporter proteins.
      R
      •
      MIT License
      •2•1•5•0•Updated May 4, 2022May 4, 2022

    • bioinformatics-group

      Public
      A Place to organize what we have
      MIT License
      •0•0•2•0•Updated Nov 30, 2021Nov 30, 2021

    • reproducibility-bioinfo

      Public
      A repo for reproducibility studies in bioinformatics
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Jun 30, 2021Jun 30, 2021

    • seq-align

      Public
      Fast, portable C implementations of Needleman-Wunsch and Smith-Waterman sequence alignment
      C
      •40•0•0•0•Updated Mar 18, 2021Mar 18, 2021

    • TportHMM

      Public
      Python
      •1•0•0•0•Updated Oct 16, 2020Oct 16, 2020

    • TranCEP

      Public
      A tool to predict the substrate class of a given transporter
      R
      •
      MIT License
      •4•5•4•1•Updated Aug 12, 2020Aug 12, 2020

    • TooT-M

      Public
      Integrative approach for detecting membrane proteins
      R
      •
      MIT License
      •1•1•1•0•Updated Jul 3, 2020Jul 3, 2020

    • Ontoclass

      Public
      Ontology-based transporter substrate annotation for benchmark datasets
      R
      •
      MIT License
      •0•0•0•0•Updated Jun 27, 2020Jun 27, 2020

    • msa_transmembraneBetaBarrel

      Public
      Multiple Sequence Alignment for Transmembrane Beta Barrel Proteins (Based on on PSI-COFFEE)
      HTML
      •1•0•0•0•Updated Jun 9, 2020Jun 9, 2020

    • tcp-follow_up

      Public
      C
      •1•0•0•0•Updated Apr 15, 2020Apr 15, 2020

    • toottc-singularity

      Public
      A singularity image for TooT-TC
      MIT License
      •0•0•0•0•Updated Apr 10, 2020Apr 10, 2020

    • TportHMM-singularity

      Public
      A Singularity image for running Shiva Shamloo/Qing Ye's Transporter Classification Tool
      Tcl
      •
      MIT License
      •0•0•5•0•Updated Mar 9, 2020Mar 9, 2020

    • ConUCSSEThesis

      Public
      A repo containing useful thesis packages
      TeX
      •0•0•1•0•Updated Mar 5, 2020Mar 5, 2020

    • BoutiquesDescriptors

      Public
      This is an open repository for Boutiques Descriptors that are under development.
      Python
      •
      MIT License
      •1•0•10•0•Updated Jun 13, 2019Jun 13, 2019

    • aqua-singularity-recipe

      Public
      A Singularity image recipe for building an image that lets anyone run AQUA.tcl and related tools easily
      Tcl
      •
      MIT License
      •1•0•0•0•Updated Jun 12, 2019Jun 12, 2019