Alternatives and similar repositories for JSTA

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

• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆35Updated last year
• linnarsson-lab / FISHscale
  Spatial analysis of FISH data
  ☆34Updated 7 months ago
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆93Updated 2 years ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆105Updated last week
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆38Updated last year
• seqscope / ficture
  ☆42Updated 2 months ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆25Updated last year
• scverse / spatialdata-io
  ☆85Updated last week
• ElementoLab / utag
  ☆40Updated last year
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆46Updated 6 months ago
• raphael-group / GASTON
  GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data
  ☆69Updated 3 weeks ago
• chenhcs / SCS
  Sub-cellular spatial transcriptomics Cell Segmentation
  ☆68Updated 2 years ago
• CaiGroup / seqFISH-PLUS
  ☆53Updated 4 years ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆84Updated last month
• fish-quant / ComSeg
  comseg
  ☆24Updated 10 months ago
• SydneyBioX / BIDCell
  Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
  ☆46Updated last year
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆47Updated last month
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆70Updated last year
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆41Updated 9 months ago
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆48Updated last week
• jian-shu-lab / Bering
  ☆24Updated 8 months ago
• nolanlab / CODEX
  Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
  ☆51Updated 3 years ago
• HiDiHlabs / ssam
  ☆27Updated last year
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆72Updated last year
• BodenmillerGroup / ImcSegmentationPipeline
  A pixel classification based multiplexed image segmentation pipeline
  ☆103Updated 2 years ago
• BodenmillerGroup / steinbock
  A toolkit for processing multiplexed tissue images
  ☆67Updated last week
• zhengli09 / BASS
  Bayesian Analytics for Spatial Segmentation
  ☆30Updated 7 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…
  ☆29Updated 2 years ago
• nolanlab / SpatialScore
  R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…
  ☆16Updated 4 years ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆47Updated 4 years ago