Alternatives and similar repositories for spapros

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

• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆61Updated 3 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆83Updated 2 weeks ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆25Updated last year
• wanglab-broad / CAST
  CAST package
  ☆40Updated last year
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆67Updated last week
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆65Updated 4 months ago
• BiomedicalMachineLearning / stlearn_interactive
  Interactive applications of stlearn
  ☆15Updated 2 years ago
• dpeerlab / ENVI
  ☆50Updated last month
• raphael-group / GASTON
  GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data
  ☆63Updated 4 months ago
• nf-core / spatialxe
  ☆23Updated last week
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆31Updated last week
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆28Updated last year
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated last month
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆40Updated 8 months ago
• theislab / multimil
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
  ☆35Updated last month
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆103Updated 4 months ago
• StatBiomed / SpatialDM
  Spatial direct messaging detected by bivariate Moran
  ☆31Updated 3 months ago
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆43Updated last week
• scverse / ecosystem-packages
  Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
  ☆30Updated this week
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆89Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 8 months ago
• simonwm / tacco
  TACCO: Transfer of Annotations to Cells and their COmbinations
  ☆61Updated 2 months ago
• scverse / spatialdata-notebooks
  ☆62Updated last week
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated this week
• prabhakarlab / Banksy_py
  ☆66Updated this week
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆43Updated 5 months ago
• BrainStOrmics / Spaco
  Spatially constrained color profiling for visualizing single-cell resolution spatial data
  ☆25Updated last year
• bhuvad / SpaNorm
  R package for normalisation of spatial transcriptomics data
  ☆14Updated 4 months ago
• ElementoLab / utag
  ☆39Updated last year
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆16Updated last month