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

  •2626 forks•230230 stars•22 issues•1616 pull requests•Updated May 30, 2026May 30, 2026

• aestetik

  Public
  AESTETIK: Convolutional autoencoder for learning spot representations from spatial transcriptomics and morphology data

  machine-learningbioinformaticsdeep-learning+ 10

  machine-learningbioinformaticsdeep-learningpytorchautoencoderrepresentation-learningsingle-celldigital-pathologycomputational-pathologymultimodal+ 3

  Jupyter Notebook

  •

  MIT License

  •55 forks•2323 stars•00 issues•00 pull requests•Updated May 30, 2026May 30, 2026

• DeepSpot

  Public
  DeepSpot: Deep learning model for predicting spatial transcriptomics from H&E histopathology images. Supports spot-level (Visium) and single-cell (Xenium) resol…

  machine-learningbioinformaticsdeep-learning+ 13

  machine-learningbioinformaticsdeep-learninggene-expressionpytorchsingle-cellcancer-researchdigital-pathologypathologycomputational-pathology+ 6

  Jupyter Notebook

  •

  MIT License

  •2020 forks•7272 stars•00 issues•00 pull requests•Updated May 29, 2026May 29, 2026

• multi-slide-aestetik-2026-analysis

  Public
  cross-patient multi-modal integration using aestetik

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 29, 2026May 29, 2026

• he2st

  Public
  Code of the paper "DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images"

  machine-learningreproducible-researchpathology+ 1

  machine-learningreproducible-researchpathologyspatial-transcriptomics

  Jupyter Notebook

  •

  MIT License

  •11 fork•1212 stars•00 issues•00 pull requests•Updated May 12, 2026May 12, 2026

• MinknoApiSimulator

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 1, 2026May 1, 2026

• stmdit

  Public
  Python

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 28, 2026Apr 28, 2026

• spladder

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

  Python

  •

  Other

  •3535 forks•113113 stars•3333 issues•11 pull request•Updated Apr 13, 2026Apr 13, 2026

• icarefm

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

  00 forks•1818 stars•33 issues•11 pull request•Updated Apr 4, 2026Apr 4, 2026

• Megatron-LM

  Public
  Ongoing research training transformer models at scale

  Python

  •

  Other

  •4k4k forks•00 stars•00 issues•00 pull requests•Updated Apr 3, 2026Apr 3, 2026

• apertus-finetuning-recipes

  Public
  Python

  •

  Apache License 2.0

  •1717 forks•00 stars•00 issues•00 pull requests•Updated Mar 28, 2026Mar 28, 2026

• collinearity

  Public
  C++

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 25, 2026Mar 25, 2026

• metagraphRF

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 24, 2026Mar 24, 2026

• NASExperiments

  Public
  Selective Sequencing Experiments

  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 23, 2026Mar 23, 2026

• DeepSpot2Cell

  Public
  DeepSpot2Cell: Predicting virtual single-cell spatial transcriptomics from H&E images using spot-level supervision

  bioinformaticsdeep-learninggene-expression+ 10

  bioinformaticsdeep-learninggene-expressionpytorchsingle-celldeconvolutioncell-segmentationdigital-pathologycomputational-pathologyspatial-transcriptomics+ 3

  Jupyter Notebook

  •

  MIT License

  •22 forks•1212 stars•55 issues•00 pull requests•Updated Mar 23, 2026Mar 23, 2026

• WiNN-for-technical-correction

  Public
  Repository accompanying the WiNN paper, containing reproducible analysis notebooks for the simulation benchmark and public multi-batch dataset, together with co…

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 19, 2026Mar 19, 2026

• winn

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

  HTML

  •

  Other

  •11 fork•00 stars•11 issue•00 pull requests•Updated Mar 12, 2026Mar 12, 2026

• sshash

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

  C++

  •

  MIT License

  •1818 forks•00 stars•00 issues•00 pull requests•Updated Mar 7, 2026Mar 7, 2026

• pthash

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

  C++

  •

  MIT License

  •3636 forks•00 stars•00 issues•00 pull requests•Updated Mar 7, 2026Mar 7, 2026

• bits

  Public
  🛠 Succinct utilities to handle bits.

  C++

  •

  MIT License

  •88 forks•00 stars•00 issues•00 pull requests•Updated Mar 6, 2026Mar 6, 2026

• essentials

  Public
  Essential C++ utilities.

  C++

  •

  MIT License

  •1010 forks•00 stars•00 issues•00 pull requests•Updated Mar 5, 2026Mar 5, 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

  •1212 forks•00 stars•00 issues•00 pull requests•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

  •11 fork•00 stars•00 issues•00 pull requests•Updated Feb 17, 2026Feb 17, 2026

• OA-VCD

  Public
  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 6, 2026Feb 6, 2026

• open-data-registry

  Public
  A registry of publicly available datasets on AWS

  Python

  •

  Apache License 2.0

  •1.2k1.2k forks•00 stars•00 issues•00 pull requests•Updated Jan 14, 2026Jan 14, 2026

• RMS

  Public
  RMS public code

  Jupyter Notebook

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•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

  •00 forks•33 stars•00 issues•00 pull requests•Updated Jan 8, 2026Jan 8, 2026

• metagraph_paper_resources

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

  Jupyter Notebook

  •00 forks•33 stars•00 issues•00 pull requests•Updated Nov 21, 2025Nov 21, 2025

• hirid2

  Public
  Documentation of the HiRID-II dataset

  Other

  •00 forks•22 stars•00 issues•00 pull requests•Updated Nov 17, 2025Nov 17, 2025

• spumoni

  Public
  Pan-Genomic Matching Statistics

  C++

  •

  GNU General Public License v3.0

  •99 forks•00 stars•00 issues•00 pull requests•Updated Nov 17, 2025Nov 17, 2025