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@ratschlab Biomedical Informatics at ETH Zurich

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    114 repositories

    • readfish

      Public
      CLI tool for flexible and fast adaptive sampling on ONT sequencers
      Python
      •
      GNU General Public License v3.0
      •35•0•0•0•Updated Mar 10, 2025Mar 10, 2025

    • metagraph

      Public
      Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
      searchassemblymetagenomicsdnagraphalignment
      C++
      •
      GNU General Public License v3.0
      •17•117•10•13•Updated Mar 10, 2025Mar 10, 2025

    • HistoPlexer

      Public
      Python
      •
      Other
      •0•0•1•0•Updated Mar 10, 2025Mar 10, 2025

    • ICMSeg

      Public
      Python
      •0•0•0•0•Updated Mar 8, 2025Mar 8, 2025

    • he2st

      Public
      Code of the paper "DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images"
      machine-learningreproducible-researchpathologyspatial-transcriptomics
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Feb 18, 2025Feb 18, 2025

    • DeepSpot

      Public
      DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images
      machine-learningpathologyspatial-transcriptomics
      Jupyter Notebook
      •
      MIT License
      •1•12•1•0•Updated Feb 18, 2025Feb 18, 2025

    • metagraph_paper_resources

      Public
      This repository contains resources related to the manuscript describing the MetaGraph framework
      Jupyter Notebook
      •0•1•0•0•Updated Feb 16, 2025Feb 16, 2025

    • immunopepper

      Public
      Code for the ImmunoPepper project
      Python
      •
      Other
      •1•2•2•1•Updated Feb 5, 2025Feb 5, 2025

    • sshash

      Public
      A compressed, associative, exact, and weighted dictionary for k-mers.
      C++
      •
      MIT License
      •18•0•0•1•Updated Dec 9, 2024Dec 9, 2024

    • tools-project-archives

      Public
      A commandline tool to create and handle project archives
      Python
      •
      MIT License
      •1•0•5•1•Updated Nov 19, 2024Nov 19, 2024

    • genomic-gnn

      Public
      Repository for the paper "Learning Genomic Sequence Representations using Graph Neural Networks over De Bruijn Graph"
      Python
      •
      MIT License
      •2•5•0•0•Updated Nov 11, 2024Nov 11, 2024

    • gLM-collection

      Public
      Collection of genomic Language Models
      0•1•0•0•Updated Nov 8, 2024Nov 8, 2024

    • nanotron-petagraph

      Public
      Minimalistic large language model 3D-parallelism training - Forked to train Petagraph
      Python
      •
      Apache License 2.0
      •164•0•0•0•Updated Nov 6, 2024Nov 6, 2024

    • circEWS

      Public
      circEWS public code
      Python
      •
      MIT License
      •24•67•4•0•Updated Oct 30, 2024Oct 30, 2024

    • phd-thesis-amir

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 26, 2024Oct 26, 2024

    • spladder

      Public
      Tool for the detection and quantification of alternative splicing events from RNA-Seq data.
      Python
      •
      Other
      •33•106•32•0•Updated Oct 9, 2024Oct 9, 2024

    • gromics

      Public
      Collection of tools and utilities for *omics analyses
      Python
      •
      MIT License
      •0•1•0•1•Updated Aug 5, 2024Aug 5, 2024

    • RMS

      Public
      RMS public code
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 29, 2024Jul 29, 2024

    • projects2019-boosting-bbvi-pyro

      Public
      Python
      •
      MIT License
      •0•0•3•2•Updated Jul 25, 2024Jul 25, 2024

    • AKI-EWS

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jul 17, 2024Jul 17, 2024

    • medical-reports-deidentification

      Public
      Java
      •
      MIT License
      •2•0•0•1•Updated Jun 11, 2024Jun 11, 2024

    • aestetik

      Public
      AESTETIK: AutoEncoder for Spatial Transcriptomics Expression with Topology and Image Knowledge
      machine-learningspatial-transcriptomics
      Python
      •0•12•0•0•Updated Jun 7, 2024Jun 7, 2024

    • simulate_spatial_transcriptomics_tool

      Public
      Simulate spatial transcriptomics data
      machine-learningspatial-transcriptomics
      Jupyter Notebook
      •0•2•0•0•Updated Jun 7, 2024Jun 7, 2024

    • st-rep

      Public
      Code of the paper "Representation learning for multi-modal spatially resolved transcriptomics data"
      machine-languagespatial-transcriptomics
      Jupyter Notebook
      •0•1•0•0•Updated Jun 7, 2024Jun 7, 2024

    • ricu

      Public
      🏥 ICU data with R 🏥
      R
      •
      GNU General Public License v3.0
      •11•0•1•0•Updated Apr 19, 2024Apr 19, 2024

    • pmvae

      Public
      Code for pmVAE model, seen in ICML CompBio '21
      Jupyter Notebook
      •
      MIT License
      •0•12•0•0•Updated Apr 12, 2024Apr 12, 2024

    • M.Sc.-thesis-Marc-Egli-Inf-Extr

      Public
      This GitHub Repo contains all the code for the Master Thesis Utilizing Deep Language Models for the Medical Information Extraction. The data is on a secure cluster.
      Jupyter Notebook
      •1•0•0•0•Updated Apr 7, 2024Apr 7, 2024

    • mla

      Public
      Scripts and data for reproducing the results of MetaGraph-MLA
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Mar 28, 2024Mar 28, 2024

    • famews

      Public
      FAMEWS: A Fairness Auditing tool for Medical Early-Warning Systems
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 19, 2024Mar 19, 2024

    • sim_read_until

      Public
      Simulator of an ONT device with ReadUntil gRPC support
      Jupyter Notebook
      •
      MIT License
      •1•6•0•0•Updated Mar 6, 2024Mar 6, 2024