Repositories list

• metagraph

  Public
  Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

  searchrna-seqgenomics+ 7

  searchrna-seqgenomicsgraphassemblymetagenomicsindexingdnaalignmentamino-acids

  C++

  •

  GNU General Public License v3.0

  •26•222•0•16•Updated Mar 7, 2026Mar 7, 2026

• sshash

  Public
  A compressed, associative, exact, and weighted dictionary for k-mers.

  C++

  •

  MIT License

  •18•0•0•0•Updated Mar 7, 2026Mar 7, 2026

• pthash

  Public
  ✈️ PTHash is a fast and compact minimal perfect hash function.

  C++

  •

  MIT License

  •36•0•0•0•Updated Mar 7, 2026Mar 7, 2026

• bits

  Public
  🛠 Succinct utilities to handle bits.

  C++

  •

  MIT License

  •8•0•0•0•Updated Mar 6, 2026Mar 6, 2026

• metagraphRF

  Public
  C++

  •0•0•0•0•Updated Mar 6, 2026Mar 6, 2026

• essentials

  Public
  Essential C++ utilities.

  C++

  •

  MIT License

  •10•0•0•0•Updated Mar 5, 2026Mar 5, 2026

• NASExperiments

  Public
  Selective Sequencing Experiments

  Python

  •1•0•0•0•Updated Mar 5, 2026Mar 5, 2026

• winn

  Public
  R package for metabolomics data correction using a multi-step pipeline

  HTML

  •

  Other

  •1•0•0•0•Updated Mar 3, 2026Mar 3, 2026

• RawHash

  Public
  RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-time without…

  C

  •

  GNU General Public License v3.0

  •11•0•0•0•Updated Mar 2, 2026Mar 2, 2026

• IMB_Amplicon_Pipeline

  Public
  Code from the GENERAL_METAB_ANALYSIS_PAN pipeline.

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• MinknoApiSimulator

  Public
  Python

  •0•0•0•0•Updated Feb 16, 2026Feb 16, 2026

• OA-VCD

  Public
  MIT License

  •0•0•0•0•Updated Feb 6, 2026Feb 6, 2026

• DeepSpot2Cell

  Public
  DeepSpot2Cell: Predicting Virtual Single-Cell Spatial Transcriptomics from H&E images using Spot-Level Supervision

  deconvolutionspatial-transcriptomics

  deconvolutionspatial-transcriptomics

  Jupyter Notebook

  •

  MIT License

  •2•8•5•0•Updated Feb 4, 2026Feb 4, 2026

• DeepSpot

  Public
  DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images

  machine-learningpathologyspatial-transcriptomics

  machine-learningpathologyspatial-transcriptomics

  Jupyter Notebook

  •

  MIT License

  •18•64•1•2•Updated Feb 4, 2026Feb 4, 2026

• multi-slide-aestetik-2026-analysis

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jan 19, 2026Jan 19, 2026

• open-data-registry

  Public
  A registry of publicly available datasets on AWS

  Python

  •

  Apache License 2.0

  •1.1k•0•0•0•Updated Jan 14, 2026Jan 14, 2026

• RMS

  Public
  RMS public code

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jan 9, 2026Jan 9, 2026

• st-rep

  Public
  Code of the paper "Representation learning for multi-modal spatially resolved transcriptomics data"

  machine-languagespatial-transcriptomics

  machine-languagespatial-transcriptomics

  Jupyter Notebook

  •0•3•0•0•Updated Jan 8, 2026Jan 8, 2026

• icarefm

  Public
  Root repository for ICareFM: "A Foundation Model for Intensive Care Unlocking Generalization across Tasks and Domains at Scale"

  0•14•2•1•Updated Dec 2, 2025Dec 2, 2025

• metagraph_paper_resources

  Public
  This repository contains resources related to the manuscript describing the MetaGraph framework

  Jupyter Notebook

  •0•3•0•0•Updated Nov 21, 2025Nov 21, 2025

• hirid2

  Public
  Documentation of the HiRID-II dataset

  Other

  •0•2•0•0•Updated Nov 17, 2025Nov 17, 2025

• spumoni

  Public
  Pan-Genomic Matching Statistics

  C++

  •

  GNU General Public License v3.0

  •9•0•0•0•Updated Nov 17, 2025Nov 17, 2025

• metagraph-examples

  Public
  Examples demonstrating how to use MetaGraph as a C++ library

  CMake

  •0•1•0•0•Updated Nov 15, 2025Nov 15, 2025

• collinearity

  Public
  C++

  •0•0•0•0•Updated Nov 12, 2025Nov 12, 2025

• feature-group-discovery

  Public
  0•0•0•0•Updated Nov 10, 2025Nov 10, 2025

• aestetik

  Public
  AESTETIK: AutoEncoder for Spatial Transcriptomics Expression with Topology and Image Knowledge

  machine-learningspatial-transcriptomics

  machine-learningspatial-transcriptomics

  Python

  •4•18•0•0•Updated Sep 25, 2025Sep 25, 2025

• projects2020_ohsu

  Public
  OHSU collaboration

  Jupyter Notebook

  •0•0•0•0•Updated Sep 13, 2025Sep 13, 2025

• metagraph-open-data

  Public
  Metagraph Open Data and Query on AWS

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •3•10•0•1•Updated Aug 17, 2025Aug 17, 2025

• spladder

  Public
  Tool for the detection and quantification of alternative splicing events from RNA-Seq data.

  Python

  •

  Other

  •35•111•33•0•Updated Jul 23, 2025Jul 23, 2025

• immunopepper_analysis

  Public
  Analyses for ImmunoPepper paper

  Jupyter Notebook

  •0•0•0•0•Updated Jul 17, 2025Jul 17, 2025