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  1. SwitchFinder SwitchFinder Public

    Python 19 1

  2. pypage pypage Public

    python implementation of the PAGE algorithm

    Python 18 3

  3. pyteiser pyteiser Public

    Python implementation of TEISER also capable of using SHAPE structural probing data

    Python 12 10

  4. Ribolog Ribolog Public

    A suite of regression-based tools for ribosome profiling data analysis

    Jupyter Notebook 9 1

  5. APAlog APAlog Public

    A tool for quantification of alternative poly A usage

    R 6 1

  6. cdsFM cdsFM Public

    cdsFM: Repository of Codon-based Foundation Models

    Python 6 1

Repositories

Showing 10 of 33 repositories
  • GENEVA Public

    Analysis pipeline for GENEVA

    goodarzilab/GENEVA’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Nov 30, 2025
  • mach-1 Public

    Mach-1: Learning transcriptome architecture from sequence with a long-context RNA foundation model

    goodarzilab/mach-1’s past year of commit activity
    Python 0 MIT 1 0 0 Updated Nov 25, 2025
  • Pan-oncRNA Public
    goodarzilab/Pan-oncRNA’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Nov 4, 2025
  • GreyHound Public

    A deep learning model for RNA stability prediction

    goodarzilab/GreyHound’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Sep 1, 2025
  • MolMiR-1 Public

    Machine learning framework for molecular miRNA target prediction

    goodarzilab/MolMiR-1’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Jul 20, 2025
  • mach-1.5-savanna Public

    Mach-1.5 model training framework built on Savanna, supporting multi-species, hybrid convolutional architectures with preprocessed RefSeq data.

    goodarzilab/mach-1.5-savanna’s past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Jul 15, 2025
  • RhoFold_benchmarking Public Forked from ml4bio/RhoFold
    goodarzilab/RhoFold_benchmarking’s past year of commit activity
    Python 0 Apache-2.0 25 0 0 Updated May 29, 2025
  • pyteiser Public

    Python implementation of TEISER also capable of using SHAPE structural probing data

    goodarzilab/pyteiser’s past year of commit activity
    Python 12 MIT 10 4 1 Updated Jan 7, 2025
  • cdsFM Public

    cdsFM: Repository of Codon-based Foundation Models

    goodarzilab/cdsFM’s past year of commit activity
    Python 6 MIT 1 7 0 Updated Oct 15, 2024
  • SwitchFinder Public
    goodarzilab/SwitchFinder’s past year of commit activity
    Python 19 MIT 1 2 0 Updated Jul 16, 2024
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