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

• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆71Updated 2 years ago
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆63Updated 11 months ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆43Updated 3 years ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆71Updated 4 months ago
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆107Updated 2 months ago
• YosefLab / popV
  ☆78Updated last week
• LungCellAtlas / HLCA_reproducibility
  This repository contains all code used for the Human Lung Cell Atlas project.
  ☆49Updated last year
• jfnavarro / st_pipeline
  ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …
  ☆84Updated 3 months ago
• matanhofree / crc-immune-hubs
  Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organiz…
  ☆39Updated 3 years ago
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆126Updated 3 weeks ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆60Updated last year
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆75Updated 3 months ago
• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆52Updated last month
• BostonGene / MFP
  Mollecular Functional Portraits
  ☆41Updated last year
• Sanofi-Public / enact-pipeline
  Repository for ENACT pipeline for end-to-end analysis of Visium HD data
  ☆51Updated last week
• Yelab2020 / Cottrazm
  Construct Tumor Transition Zone Microenvironment
  ☆44Updated 7 months ago
• navinlabcode / CellTrek
  ☆120Updated 3 years ago
• elixir-europe-training / ELIXIR-SCO-spatial-omics
  ☆38Updated 2 months ago
• immunogenomics / LISI
  Methods to compute Local Inverse Simpson's Index (LISI)
  ☆62Updated 3 years ago
• icbi-lab / luca
  Single-cell Lung Cancer Atlas with 1.2M cells
  ☆63Updated 5 months ago
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆69Updated last year
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆129Updated 4 months ago
• snehamitra / SCARlink
  ☆52Updated 9 months ago
• tiroshlab / 3ca
  Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".
  ☆116Updated 9 months ago
• Nanostring-Biostats / SpatialDecon
  The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This al…
  ☆39Updated last month
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆73Updated 4 months ago
• multitalk / awesome-cell-cell-communication
  Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics
  ☆50Updated 2 weeks ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆110Updated last month
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆73Updated 10 months ago
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆112Updated last week