Alternatives and similar repositories for CODA

Users that are interested in CODA are comparing it to the libraries listed below

• maxpmx / CelloType

  View on GitHub
  End-to-end model for cell segmentation and classification
  ☆23Jan 13, 2025Updated last year
• davidliwei / PS

  View on GitHub
  Perturbation-response Score (PS) analysis is a method to quantify diverse perturbation responses and discover novel biological insights i…
  ☆17Apr 20, 2024Updated last year
• HTGenomeAnalysisUnit / nf-pipeline-regenie

  View on GitHub
  GWAS and rare variants tests at high speed using regenie
  ☆16Jan 9, 2026Updated last month
• labsyspharm / palom

  View on GitHub
  Piecewise alignment for layers of mosaics
  ☆35Sep 2, 2025Updated 5 months ago
• PansccSpat / SpatialMapESCC

  View on GitHub
  ☆24Oct 31, 2024Updated last year
• Teddy-XiongGZ / DeepGSEA

  View on GitHub
  ☆17Jul 13, 2024Updated last year
• mahmoodlab / TriPath

  View on GitHub
  Analysis of 3D pathology samples using weakly supervised AI - Cell
  ☆113Jan 24, 2025Updated last year
• schwartzlab-methods / CellNEST

  View on GitHub
  Implementation of CellNEST method
  ☆59Feb 6, 2026Updated last week
• labsyspharm / orion-crc

  View on GitHub
  ☆27Jun 24, 2025Updated 7 months ago
• kevindehaan / stain-transformation

  View on GitHub
  ☆46Jan 10, 2022Updated 4 years ago
• KimiaLabMayo / KimiaNet

  View on GitHub
  A Trained Network for Histopathology Image Representation
  ☆22Jun 6, 2024Updated last year
• BodenmillerGroup / imcRtools

  View on GitHub
  An R package for handling and analysing imaging mass cytometry data
  ☆29Jan 6, 2026Updated last month
• aifimmunology / aifi-healthy-pbmc-reference

  View on GitHub
  Assembly and Annotation of the Human Immune Health Atlas
  ☆20Aug 28, 2025Updated 5 months ago
• qupath / qupath-extension-omero-web

  View on GitHub
  QuPath extension to work with images through OMERO's web API
  ☆10May 31, 2024Updated last year
• cpathology / NucleiSegHE

  View on GitHub
  H&E ROI-Level and WSI-Level Nuclei Segmentation with HoVer-Net
  ☆10Jul 30, 2024Updated last year
• jeongdo801 / scNOVA

  View on GitHub
  scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis
  ☆11Jul 29, 2023Updated 2 years ago
• HMS-IDAC / UnMicst

  View on GitHub
  UNet script, model, sample data
  ☆14Feb 19, 2025Updated 11 months ago
• broadchenf / Slide-tags

  View on GitHub
  ☆12Apr 4, 2023Updated 2 years ago
• SydneyBioX / HEtoSGEBench

  View on GitHub
  ☆18Feb 5, 2025Updated last year
• ArnaudAbreu / DiagFLFH

  View on GitHub
  code related to submission of "Accurate diagnosis of lymphoma on whole slide histopathology images using deep learning"
  ☆10May 12, 2020Updated 5 years ago
• jianhuupenn / MorphLink

  View on GitHub
  MorphLink: Bridging Cellular Morphological Behaviors and Molecular Dynamics in Multi-modal Spatial Omics
  ☆16Dec 7, 2025Updated 2 months ago
• STOmics / ST-GEARS

  View on GitHub
  A Spatial Transcriptomics Geospatial Profile Recovery System Tool through Anchors
  ☆19Jul 24, 2025Updated 6 months ago
• kaiko-ai / Midnight

  View on GitHub
  Midnight - Pathology foundation models trained on orders of magnitude fewer WSIs
  ☆29Nov 22, 2025Updated 2 months ago
• kmboehm / orpheus

  View on GitHub
  ☆16Feb 18, 2025Updated 11 months ago
• bowang-lab / DeepVelo

  View on GitHub
  ☆48Feb 7, 2024Updated 2 years ago
• SydneyBioX / GHIST

  View on GitHub
  ☆63Sep 16, 2025Updated 4 months ago
• danro9685 / ASCETIC

  View on GitHub
  ASCETIC (Agony-baSed Cancer EvoluTion InferenCe) is a novel framework for the inference of a set of statistically significant temporal pa…
  ☆12Apr 18, 2025Updated 9 months ago
• coskunlab / scSpaMet

  View on GitHub
  ☆12Sep 29, 2023Updated 2 years ago
• elizabethdorans / pgBoost

  View on GitHub
  ☆16Oct 23, 2025Updated 3 months ago
• chaudatascience / channel_adaptive_models

  View on GitHub
  CHAMMI: A benchmark for channel-adaptive models in microscopy imaging
  ☆14Oct 23, 2024Updated last year
• OSU-BMBL / scGNN2.0

  View on GitHub
  ☆12Dec 4, 2023Updated 2 years ago
• azizilab / DIISCO_public

  View on GitHub
  Publically accessible code for DIISCO method
  ☆12Oct 15, 2025Updated 3 months ago
• BoomStarcuc / GeneSegNet

  View on GitHub
  ☆17Dec 7, 2023Updated 2 years ago
• pearcetm / svs-deidentifier

  View on GitHub
  Strip potentially identifying label and macro images from Aperio SVS whole slide image files
  ☆37Apr 29, 2024Updated last year
• DIAGNijmegen / pathology-artifact-detection

  View on GitHub
  Quality control of whole-slide images through multi-class semantic segmentation of artifacts
  ☆38Jan 25, 2024Updated 2 years ago
• Graph-and-Geometric-Learning / STFlow

  View on GitHub
  Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching, ICML2025 (Spotlight)
  ☆27Aug 11, 2025Updated 6 months ago
• ding-lab / mushroom

  View on GitHub
  A computational tool for identification of 3D multi-modal spatial neighborhoods
  ☆15Aug 1, 2025Updated 6 months ago
• DeepMIALab / PathoSeg

  View on GitHub
  ☆20Jul 2, 2023Updated 2 years ago
• MarioniLab / oor_design_reproducibility

  View on GitHub
  ☆16Sep 1, 2023Updated 2 years ago