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

• 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 8 months ago
• YMa-lab / CARD
  ☆127Updated last year
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆125Updated last month
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆136Updated 8 months ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 8 months ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆121Updated 6 months ago
• navinlabcode / CellTrek
  ☆126Updated 3 years ago
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆70Updated last year
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆83Updated 2 years ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆81Updated 7 months ago
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆128Updated last week
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆141Updated this week
• almaan / stereoscope
  Spatial mapping of cell types by integration of transcriptomics data
  ☆98Updated 3 years ago
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆114Updated last week
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆67Updated last week
• Sanofi-Public / enact-pipeline
  Repository for ENACT pipeline for end-to-end analysis of Visium HD data
  ☆69Updated 5 months ago
• YosefLab / popV
  ☆83Updated this week
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆77Updated 2 months ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆180Updated 2 years ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆106Updated 2 years ago
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆119Updated last year
• simonwm / tacco
  TACCO: Transfer of Annotations to Cells and their COmbinations
  ☆61Updated 2 months ago
• jaleesr / SenePy
  SenePy is a set of tools to score single-cells based on their expression of cell-specific senescence markers. Please see the following pu…
  ☆45Updated 9 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆79Updated 9 months ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆105Updated last year
• elixir-europe-training / ELIXIR-SCO-spatial-omics
  ☆45Updated 7 months ago
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆135Updated 2 years 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".
  ☆120Updated last year
• favilaco / deconv_benchmark
  ☆58Updated 4 years ago
• 10XGenomics / HumanColonCancer_VisiumHD
  Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…
  ☆102Updated 5 months ago