Alternatives and similar repositories for cellcharter:

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

• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆85Updated 3 months ago
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆123Updated 3 weeks ago
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆56Updated 4 months ago
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆45Updated 8 months ago
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆92Updated last week
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆86Updated last month
• theislab / spatial_scog_workshop_2022
  Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
  ☆52Updated 2 years ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆59Updated 8 months ago
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆109Updated last year
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆33Updated 10 months ago
• data2intelligence / SpaCET
  Spatial Cellular Estimator for Tumors
  ☆49Updated last week
• almaan / stereoscope
  Spatial mapping of cell types by integration of transcriptomics data
  ☆89Updated 2 years ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆63Updated 3 weeks 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 …
  ☆74Updated last week
• azizilab / starfysh
  Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology
  ☆111Updated 6 months ago
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆75Updated last year
• navinlabcode / CellTrek
  ☆114Updated 2 years ago
• zhengli09 / BASS
  Bayesian Analytics for Spatial Segmentation
  ☆25Updated 5 months ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆99Updated last year
• zcang / COMMOT
  ☆109Updated 10 months ago
• shuxiaoc / maxfuse
  ☆49Updated 9 months ago
• dpeerlab / ENVI
  ☆45Updated 4 months ago
• LungCellAtlas / HLCA_reproducibility
  This repository contains all code used for the Human Lung Cell Atlas project.
  ☆49Updated last year
• 10XGenomics / HumanColonCancer_VisiumHD
  Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…
  ☆48Updated 3 weeks ago
• Nanostring-Biostats / CosMx-Analysis-Scratch-Space
  This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…
  ☆56Updated this week
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆40Updated 3 years ago
• nolanlab / CODEX
  Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
  ☆45Updated 2 years ago
• ShobiStassen / VIA
  trajectory inference
  ☆96Updated last month
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆102Updated last year
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆67Updated 2 years ago