Alternatives and similar repositories for Spaco

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

• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆29Updated last year
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆67Updated last month
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆64Updated 3 weeks ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆47Updated last month
• wanglab-broad / CAST
  CAST package
  ☆41Updated last year
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆65Updated 5 months ago
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 2 months ago
• theislab / troutpy
  Package for the analysis of Transcripts outside segmented cells in ST data
  ☆23Updated last week
• jbergenstrahle / STUtility
  ☆53Updated 2 years ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆77Updated 10 months ago
• klarman-cell-observatory / hdst
  ☆19Updated 6 years ago
• raphael-group / GASTON
  GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data
  ☆69Updated 3 weeks ago
• Wei-BioMath / NeuronChat
  ☆41Updated 2 years ago
• rargelaguet / mouse_organogenesis_10x_multiome_publication
  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""
  ☆40Updated 3 years ago
• linnarsson-lab / developing-human-brain
  ☆36Updated 2 months ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆38Updated last month
• gerstung-lab / BaSISS
  Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
  ☆27Updated 3 years 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…
  ☆66Updated 4 months ago
• AllenInstitute / scrattch.bigcat
  iterative clustering pipeline of big single cell datasets.
  ☆35Updated 3 months ago
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆41Updated 9 months ago
• theislab / multimil
  Weakly supervised learning uncovers phenotypic signatures in single-cell data
  ☆37Updated 2 weeks ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated 3 weeks ago
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆56Updated 7 months ago
• rajewsky-lab / spacemake
  ☆48Updated this week
• pengminshi / MRtree
  MRtree R implementation
  ☆12Updated 2 years ago
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆44Updated 4 months ago
• nf-core / spatialxe
  ☆24Updated last month
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆45Updated 7 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆83Updated 9 months ago
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆62Updated last year