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.
  ☆70Updated 2 years ago
• jacoblevine / PhenoGraph
  Subpopulation detection in high-dimensional single-cell data
  ☆141Updated 5 years ago
• scverse / rapids_singlecell
  rapids_singlecell: GPU-accelerated framework for scRNA analysis
  ☆281Updated this week
• HiDiHlabs / ssam
  ☆27Updated last year
• gustaveroussy / sopa
  Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…
  ☆251Updated this week
• scverse / muon
  muon is a multimodal omics Python framework
  ☆256Updated last week
• scverse / spatialdata
  An open and interoperable data framework for spatial omics data
  ☆332Updated last week
• dpeerlab / Palantir
  Single cell trajectory detection
  ☆282Updated 3 weeks ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆105Updated 5 months ago
• emanuega / MERlin
  MERlin is an extensible analysis pipeline applied to decoding MERFISH data
  ☆35Updated 4 years ago
• whitews / FlowKit
  A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces
  ☆194Updated last month
• scverse / pertpy
  Single-cell perturbation analysis
  ☆218Updated this week
• Teichlab / bbknn
  Batch balanced KNN
  ☆176Updated 2 years ago
• kharchenkolab / Baysor
  Bayesian Segmentation of Spatial Transcriptomics Data
  ☆200Updated last year
• beliveau-lab / PaintSHOP_pipeline
  A scalable machine learning pipeline for probe specificity prediction.
  ☆14Updated last year
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆243Updated last year
• ZhuangLab / MERFISH_analysis
  Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.
  ☆50Updated 4 years ago
• scverse / squidpy
  Spatial Single Cell Analysis in Python
  ☆543Updated this week
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆205Updated last month
• labsyspharm / mcmicro
  Multiple-choice microscopy pipeline
  ☆144Updated 3 weeks ago
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆104Updated last week
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆149Updated last year
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆242Updated this week
• theislab / paga
  Mapping out the coarse-grained connectivity structures of complex manifolds.
  ☆231Updated 5 years ago
• dpeerlab / PhenoGraph
  Subpopulation detection in high-dimensional single-cell data
  ☆72Updated 5 years ago
• AllenInstitute / cell_type_mapper
  Repository for storing prototype functionality implementations for the BKP
  ☆38Updated last week
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆174Updated 2 months ago
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆251Updated last week
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆114Updated last week
• linnarsson-lab / loompy
  Python implementation of the Loom file format - http://loompy.org
  ☆148Updated last year