Alternatives and similar repositories for spatial_scog_workshop_2022

Users that are interested in spatial_scog_workshop_2022 are comparing it to the libraries listed below

• YMa-lab / CARD
  ☆129Updated last year
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆88Updated 3 years ago
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆134Updated 3 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 …
  ☆88Updated last week
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆138Updated 11 months ago
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆132Updated 3 months ago
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆149Updated 2 weeks ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆187Updated 3 weeks ago
• almaan / stereoscope
  Spatial mapping of cell types by integration of transcriptomics data
  ☆100Updated 3 years ago
• navinlabcode / CellTrek
  ☆129Updated 3 years ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆81Updated 11 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆81Updated last year
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆127Updated 8 months ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆106Updated last year
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆123Updated last year
• elixir-europe-training / ELIXIR-SCO-spatial-omics
  ☆45Updated 9 months ago
• Sanofi-Public / enact-pipeline
  Repository for ENACT pipeline for end-to-end analysis of Visium HD data
  ☆72Updated 7 months ago
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆117Updated 3 months ago
• 10XGenomics / HumanColonCancer_VisiumHD
  Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…
  ☆109Updated 7 months ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆79Updated this week
• favilaco / deconv_benchmark
  ☆59Updated 5 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆178Updated 10 months ago
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆73Updated last year
• tiroshlab / 3ca
  Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".
  ☆131Updated last year
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆95Updated last week
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆84Updated 10 months ago
• Swarbricklab-code / BrCa_cell_atlas
  Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".
  ☆125Updated last year
• YosefLab / popV
  ☆87Updated last week
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆107Updated 2 years ago
• simonwm / tacco
  TACCO: Transfer of Annotations to Cells and their COmbinations
  ☆62Updated 5 months ago