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    30 repositories

    • mach-1.5-savanna

      Public
      Mach-1.5 model training framework built on Savanna, supporting multi-species, hybrid convolutional architectures with preprocessed RefSeq data.
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 15, 2025Jul 15, 2025

    • UTRCellType_Prediction_Design

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 29, 2025Jun 29, 2025

    • mach-1

      Public
      Mach-1: A long-context RNA foundation model for predicting transcriptome architecture. Training pipeline and model weights.
      Python
      •
      MIT License
      •3•4•1•1•Updated Mar 11, 2025Mar 11, 2025

    • pyteiser

      Public
      Python implementation of TEISER also capable of using SHAPE structural probing data
      Python
      •
      MIT License
      •9•12•4•1•Updated Jan 7, 2025Jan 7, 2025

    • cdsFM

      Public
      cdsFM: Repository of Codon-based Foundation Models
      Python
      •
      MIT License
      •1•5•7•0•Updated Oct 15, 2024Oct 15, 2024

    • Pan-oncRNA

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 17, 2024Jul 17, 2024

    • SwitchFinder

      Public
      Python
      •
      MIT License
      •1•18•2•0•Updated Jul 16, 2024Jul 16, 2024

    • goodarzilab.github.io

      Public
      Lab website
      HTML
      •1•0•0•0•Updated Jul 15, 2024Jul 15, 2024

    • RBP_modules

      Public
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 6, 2024Jun 6, 2024

    • pypage

      Public
      python implementation of the PAGE algorithm
      Python
      •
      MIT License
      •3•17•17•0•Updated Apr 30, 2024Apr 30, 2024

    • DMS-tutorial

      Public
      Assorted scripts for processing DMS-Seq data
      HTML
      •0•2•0•0•Updated Jan 31, 2024Jan 31, 2024

    • Abe

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jan 4, 2024Jan 4, 2024

    • OpenTrons_2

      Public
      Repository for OpenTrons code
      Python
      •
      MIT License
      •0•0•0•0•Updated May 28, 2023May 28, 2023

    • IRIS

      Public
      Notebook for identification of RNA antisense species (IRIS)
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Mar 23, 2023Mar 23, 2023

    • pythia

      Public
      Scripts for training and predicting binding of RBPs
      Jupyter Notebook
      •0•1•0•0•Updated Feb 23, 2023Feb 23, 2023

    • Ribolog

      Public
      A suite of regression-based tools for ribosome profiling data analysis
      Jupyter Notebook
      •
      MIT License
      •1•9•3•0•Updated Oct 3, 2022Oct 3, 2022

    • WES

      Public
      A Whole Exome Sequencing (WES) analysis workflow
      Shell
      •
      MIT License
      •0•3•2•0•Updated Jul 25, 2022Jul 25, 2022

    • ciberatac

      Public
      CiberATAC public repository
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Apr 15, 2022Apr 15, 2022

    • iAnalyzer

      Public
      An analytical pipeline for powered analysis of CRISPR screens
      Python
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Apr 11, 2022Apr 11, 2022

    • APAlog

      Public
      A tool for quantification of alternative poly A usage
      R
      •
      MIT License
      •1•5•0•0•Updated Feb 21, 2022Feb 21, 2022

    • Basenji-Pytorch

      Public
      Jupyter Notebook
      •1•4•0•0•Updated Jan 14, 2022Jan 14, 2022

    • opentrons

      Public
      Python
      •0•0•0•0•Updated Sep 20, 2021Sep 20, 2021

    • dms_utils

      Public
      khorms functions for dms data processing
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 27, 2021Apr 27, 2021

    • MicrotRNA

      Public
      Using k-mer deconvolution for rapid clustering of sequences into highly similar group and collapsing each group to tRNA families.
      Python
      •0•0•0•0•Updated Sep 21, 2020Sep 21, 2020

    • PRADA

      Public
      Prioritization of Regulatory Pathways based on Analysis of RNA Dynamics Alterations
      Jupyter Notebook
      •2•0•0•0•Updated Mar 27, 2020Mar 27, 2020

    • matRseq

      Public
      mature tRNA sequencing
      Python
      •0•0•0•0•Updated Sep 23, 2019Sep 23, 2019

    • riboprofiler

      Public
      A set of tools for ribo-seq analysis
      Python
      •0•0•0•0•Updated Apr 18, 2018Apr 18, 2018

    • TEISER

      Public
      Tool for Eliciting Informative Structural Elements in RNA
      HTML
      •2•0•0•0•Updated Apr 19, 2017Apr 19, 2017

    • FIRE

      Public
      Finding Informative Regulatory Elements
      Roff
      •
      Other
      •1•0•0•0•Updated Jul 22, 2016Jul 22, 2016

    • PAGE

      Public
      Pathway Analysis of Gene Expression
      Perl
      •1•0•0•0•Updated Mar 11, 2015Mar 11, 2015