Alternatives and similar repositories for starfish

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

• fish-quant / big-fish
  Toolbox for the analysis of smFISH images.
  ☆68Updated last year
• scverse / rapids_singlecell
  rapids_singlecell: GPU-accelerated framework for scRNA analysis
  ☆219Updated this week
• cytoflow / cytoflow
  A Python toolbox for quantitative, reproducible flow cytometry analysis
  ☆196Updated last week
• kharchenkolab / Baysor
  Bayesian Segmentation of Spatial Transcriptomics Data
  ☆181Updated 7 months ago
• scverse / spatialdata
  An open and interoperable data framework for spatial omics data
  ☆291Updated this week
• gustaveroussy / sopa
  Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…
  ☆205Updated last week
• jacoblevine / PhenoGraph
  Subpopulation detection in high-dimensional single-cell data
  ☆138Updated 4 years ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆92Updated 2 weeks ago
• whitews / FlowKit
  A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces
  ☆179Updated 3 weeks ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆239Updated 4 months ago
• HiDiHlabs / ssam
  ☆27Updated 9 months ago
• labsyspharm / mcmicro
  Multiple-choice microscopy pipeline
  ☆133Updated 4 months ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆234Updated last week
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆199Updated 4 months ago
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆104Updated last week
• yuqiyuqitan / SPACEc
  ☆45Updated 3 weeks ago
• broadinstitute / Tangram
  Spatial alignment of single cell transcriptomic data.
  ☆306Updated 2 weeks ago
• scverse / napari-spatialdata
  Interactive visualization of spatial omics data
  ☆61Updated last week
• dpeerlab / PhenoGraph
  Subpopulation detection in high-dimensional single-cell data
  ☆69Updated 4 years ago
• scverse / squidpy
  Spatial Single Cell Analysis in Python
  ☆496Updated last week
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆390Updated 3 months ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆365Updated 3 weeks ago
• dpeerlab / Palantir
  Single cell trajectory detection
  ☆254Updated 2 weeks ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆144Updated 7 months ago
• angelolab / ark-analysis
  Integrated pipeline for multiplexed image analysis
  ☆91Updated 3 months ago
• beliveau-lab / PaintSHOP_pipeline
  A scalable machine learning pipeline for probe specificity prediction.
  ☆14Updated last year
• AllenInstitute / cell_type_mapper
  Repository for storing prototype functionality implementations for the BKP
  ☆29Updated last week
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆80Updated 3 weeks ago
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆224Updated last week
• theislab / paga
  Mapping out the coarse-grained connectivity structures of complex manifolds.
  ☆223Updated 5 years ago