Alternatives and similar repositories for spatialxe

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

• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆64Updated last month
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 7 months ago
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆39Updated 3 months ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆40Updated last month
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆63Updated this week
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆16Updated 4 months ago
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆59Updated 2 weeks ago
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆115Updated this week
• AllenInstitute / cell_type_mapper
  Repository for storing prototype functionality implementations for the BKP
  ☆33Updated this week
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆27Updated last year
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆24Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 6 months ago
• theislab / multimil
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
  ☆33Updated 2 weeks ago
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆31Updated this week
• BodenmillerGroup / imcRtools
  An R package for handling and analysing imaging mass cytometry data
  ☆27Updated last month
• raphael-group / GASTON
  GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data
  ☆59Updated 2 months ago
• BrainStOrmics / Spaco
  Spatially constrained color profiling for visualizing single-cell resolution spatial data
  ☆26Updated 11 months ago
• JCVenterInstitute / NSForest
  A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA seq…
  ☆65Updated this week
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆82Updated last month
• lilab-bcb / cirrocumulus
  Bring your single-cell data to life
  ☆88Updated last week
• gerstung-lab / BaSISS
  Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
  ☆26Updated 2 years ago
• wanglab-broad / CAST
  CAST package
  ☆40Updated 10 months ago
• nolanlab / SpatialScore
  R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…
  ☆15Updated 3 years ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated 2 months ago
• MargoKapustina / XeniumSpatialAnalysis
  R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients
  ☆24Updated 3 months ago
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆86Updated last year
• klarman-cell-observatory / hdst
  ☆19Updated 5 years ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆36Updated 2 months ago
• PMBio / MuDataSeurat
  .h5mu files interface for Seurat
  ☆32Updated last year
• scverse / anndataR
  AnnData interoperability in R
  ☆93Updated this week