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

• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆102Updated last week
• pachterlab / voyager
  From geospatial to spatial -omics
  ☆85Updated 2 weeks ago
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆61Updated 2 years ago
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆110Updated 5 months ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆79Updated last year
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆86Updated 6 months ago
• Nanostring-Biostats / CellProfileLibrary
  ☆30Updated last month
• Single-Cell-Genomics-Group-CNAG-CRG / Tumor-Immune-Cell-Atlas
  Code repository for the Tumor Immune Cell Atlas (TICA) project
  ☆62Updated 2 years ago
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆69Updated 5 months ago
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆102Updated 2 years ago
• carmonalab / GeneNMF
  Methods to discover gene programs on single-cell data
  ☆99Updated 2 months ago
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆72Updated 5 months ago
• scverse / anndataR
  AnnData interoperability in R
  ☆69Updated this week
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆67Updated 2 years ago
• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆99Updated 2 years ago
• crazyhottommy / scclusteval
  Single Cell Cluster Evaluation
  ☆87Updated 3 years ago
• 10XGenomics / HumanColonCancer_VisiumHD
  Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…
  ☆46Updated 2 months ago
• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆49Updated 4 months ago
• tiroshlab / 3ca
  Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".
  ☆90Updated 5 months ago
• Coolgenome / iTALK
  ☆59Updated 5 years ago
• FelixTheStudent / cellpypes
  Cell type pipes for R
  ☆51Updated last year
• MarioniLab / scran
  Clone of the Bioconductor repository for the scran package.
  ☆41Updated 5 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆59Updated 8 months ago
• MarioniLab / miloDE
  Framework for sensitive DE testing (using neighbourhoods)
  ☆64Updated 6 months ago
• data2intelligence / CytoSig
  ☆49Updated 4 months ago
• Japrin / STARTRAC
  STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)
  ☆93Updated last year
• abelson-lab / scATOMIC
  Pan-Cancer Single Cell Classifier
  ☆64Updated 8 months ago
• RausellLab / CelliD
  Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.
  ☆93Updated last year
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆68Updated 3 weeks ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆61Updated last year