Alternatives and similar repositories for CosMx-Analysis-Scratch-Space

Users that are interested in CosMx-Analysis-Scratch-Space are comparing it to the libraries listed below

• pachterlab / voyager
  From geospatial to spatial -omics
  ☆98Updated last month
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆90Updated 2 months ago
• ludvigla / semla
  ☆94Updated last month
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆81Updated 2 years ago
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆124Updated last week
• scverse / anndataR
  AnnData interoperability in R
  ☆119Updated this week
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆81Updated 3 years ago
• abelson-lab / scATOMIC
  Pan-Cancer Single Cell Classifier
  ☆82Updated last year
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆129Updated 3 months ago
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆146Updated 2 months ago
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆75Updated last year
• saezlab / mistyR
  Multiview Intercellular SpaTial modeling framework
  ☆70Updated 4 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆80Updated 7 months ago
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆119Updated last year
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆111Updated 2 years ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆104Updated last year
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆78Updated 9 months ago
• crazyhottommy / scclusteval
  Single Cell Cluster Evaluation
  ☆97Updated 4 years ago
• MarioniLab / miloDE
  Framework for sensitive DE testing (using neighbourhoods)
  ☆73Updated this week
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆66Updated 3 weeks ago
• tiroshlab / 3ca
  Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".
  ☆127Updated last year
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆119Updated 5 months ago
• quadbio / Pando
  Multiome GRN inference.
  ☆128Updated last year
• 10XGenomics / HumanColonCancer_VisiumHD
  Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…
  ☆98Updated 4 months ago
• jfnavarro / st_pipeline
  ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …
  ☆87Updated 7 months ago
• navinlabcode / CellTrek
  ☆125Updated 3 years ago
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆38Updated 4 months ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆177Updated 2 years ago
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆133Updated 8 months ago
• Nanostring-Biostats / CellProfileLibrary
  ☆31Updated 5 months ago