Alternatives and similar repositories for proseg:

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

• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆61Updated this week
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆36Updated 4 months ago
• Nanostring-Biostats / InSituType
  An R package for performing cell typing in SMI and other single cell data
  ☆34Updated 4 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆60Updated 10 months ago
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆27Updated 7 months ago
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆26Updated 8 months 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…
  ☆62Updated this week
• nf-core / spatialxe
  ☆16Updated this week
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆116Updated 2 weeks ago
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆72Updated 2 years ago
• pachterlab / concordex
  Identification of spatial homogeneous regions
  ☆20Updated 3 months ago
• scverse / anndataR
  AnnData interoperability in R
  ☆74Updated this week
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆72Updated last month
• StatBiomed / SpatialDM
  Spatial direct messaging detected by bivariate Moran
  ☆26Updated 3 months ago
• immunitastx / monkeybread
  Analyzing cellular niches in spatial transcriptomics data
  ☆29Updated 5 months ago
• HiDiHlabs / ssam
  ☆28Updated 6 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆77Updated 2 weeks ago
• Novartis / scar
  scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
  ☆52Updated 8 months ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆40Updated 3 years ago
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆25Updated this week
• theislab / spatial_scog_workshop_2022
  Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
  ☆53Updated 2 years ago
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆53Updated 3 weeks ago
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆35Updated 11 months ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆66Updated 2 months ago
• YosefLab / popV
  ☆72Updated this week
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated 2 weeks ago
• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆52Updated 6 months ago
• rargelaguet / mouse_organogenesis_10x_multiome_publication
  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""
  ☆40Updated 2 years ago
• dpeerlab / ENVI
  ☆47Updated 2 weeks ago
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆92Updated 4 months ago