Alternatives and similar repositories for webatlas-pipeline

Users that are interested in webatlas-pipeline are comparing it to the libraries listed below

• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆114Updated this week
• nf-core / spatialxe
  ☆20Updated this week
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆40Updated last month
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆82Updated last month
• theislab / multimil
  Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
  ☆33Updated last week
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆130Updated 2 weeks ago
• scverse / spatialdata-notebooks
  ☆55Updated last week
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆21Updated 7 months ago
• rajewsky-lab / spacemake
  ☆44Updated 2 weeks ago
• shuxiaoc / maxfuse
  ☆55Updated last year
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆39Updated 3 months ago
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆37Updated 5 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆63Updated 3 weeks ago
• YosefLab / popV
  ☆82Updated last week
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆31Updated 3 weeks ago
• wanglab-broad / CAST
  CAST package
  ☆40Updated 9 months ago
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆59Updated last week
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆106Updated this week
• AllenInstitute / cell_type_mapper
  Repository for storing prototype functionality implementations for the BKP
  ☆33Updated this week
• parashardhapola / scarf
  Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…
  ☆101Updated 4 months ago
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• 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…
  ☆75Updated this week
• raphael-group / GASTON
  GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data
  ☆59Updated 2 months ago
• yuqiyuqitan / SPACEc
  ☆47Updated 2 months ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆94Updated last month
• lilab-bcb / cirrocumulus
  Bring your single-cell data to life
  ☆88Updated this week
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆44Updated 4 years ago
• elixir-europe-training / ELIXIR-SCO-spatial-omics
  ☆40Updated 4 months ago
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆98Updated 2 months ago
• 10XGenomics / janesick_nature_comms_2023_companion
  Code companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spat…
  ☆24Updated last year