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
  ☆30Updated last year
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆65Updated last week
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆69Updated 2 months ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆48Updated 2 months ago
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆45Updated 5 months ago
• linnarsson-lab / developing-human-brain
  ☆36Updated 2 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…
  ☆66Updated 4 months ago
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆41Updated 10 months ago
• wanglab-broad / CAST
  CAST package
  ☆42Updated last year
• nf-core / spatialxe
  ☆24Updated 2 months 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
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆80Updated 11 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆84Updated 10 months ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆39Updated 2 months ago
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆62Updated last year
• jbergenstrahle / STUtility
  ☆53Updated 2 years ago
• klarman-cell-observatory / hdst
  ☆19Updated 6 years ago
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆69Updated last year
• saezlab / mistyR
  Multiview Intercellular SpaTial modeling framework
  ☆71Updated last week
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated last month
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆82Updated 3 years ago
• simonwm / tacco
  TACCO: Transfer of Annotations to Cells and their COmbinations
  ☆62Updated 4 months ago
• zijianni / SpotClean
  R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
  ☆34Updated last week
• Janezjz / cellanova
  CellANOVA: Cell State Space Analysis of Variance for signal recovery in single cell batch integration
  ☆53Updated last year
• 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
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 3 months ago
• StatBiomed / SpatialDM
  Spatial direct messaging detected by bivariate Moran
  ☆32Updated 6 months ago
• rajewsky-lab / spacemake
  ☆48Updated this week
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆46Updated 8 months ago
• raphael-group / GASTON
  GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data
  ☆70Updated last month