Alternatives and similar repositories for MUSE:

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

• chenhcs / SCS
  Sub-cellular spatial transcriptomics Cell Segmentation
  ☆60Updated last year
• ElementoLab / utag
  ☆33Updated 10 months ago
• AI4SCR / ATHENA
  ☆31Updated last month
• mahmoodlab / MAPS
  Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications
  ☆50Updated 11 months ago
• ludvb / xfuse
  Super-resolved spatial transcriptomics by deep data fusion
  ☆70Updated last year
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆74Updated last month
• SydneyBioX / BIDCell
  Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
  ☆37Updated 7 months ago
• spacetx-spacejam / data
  data for spacejam2
  ☆17Updated 2 years ago
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆52Updated 8 months ago
• raphael-group / paste
  Probabilistic Alignment of Spatial Transcriptomics Experiments
  ☆84Updated last year
• wollmanlab / JSTA
  ☆14Updated 2 years ago
• CaiGroup / seqFISH-PLUS
  ☆48Updated 3 years ago
• YangLabHKUST / STitch3D
  Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices
  ☆60Updated last year
• snap-stanford / stellar
  ☆64Updated 2 years ago
• scverse / spatialdata-notebooks
  ☆41Updated this week
• MICS-Lab / novae
  Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…
  ☆30Updated this week
• YangLabHKUST / SpatialScope
  A unified approach for integrating spatial and single-cell transcriptomics data by leveraging deep generative models
  ☆58Updated 8 months ago
• romain-lopez / DestVI-reproducibility
  Reproducing the experiments of the DestVI paper
  ☆17Updated 3 years ago
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆71Updated last year
• GlastonburyC / RNAPath
  Self-supervised representation learning combining GTEx histology, RNA-seq and WGS
  ☆28Updated 5 months ago
• Weiqin-Zhao / Hist2Cell
  ☆12Updated 5 months ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆85Updated 2 weeks ago
• rajewsky-lab / openst
  Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab
  ☆88Updated 2 months ago
• nf-core / imcyto
  Image Mass Cytometry analysis pipeline
  ☆25Updated 2 weeks ago
• sggao / celllens
  CellLENS: Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data
  ☆14Updated last week
• JinmiaoChenLab / SpatialGlue
  SpatialGlue is a novel deep learning methods for spatial multi-omics data integration.
  ☆48Updated 7 months ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆39Updated 3 years ago
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆43Updated 6 months ago
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆105Updated last week
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆34Updated last year