Alternatives and similar repositories for starfish:

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

• scverse / rapids_singlecell
  Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data proces…
  ☆200Updated this week
• fish-quant / big-fish-examples
  Notebooks to illustrate how BigFISH is working.
  ☆13Updated 2 years ago
• fish-quant / big-fish
  Toolbox for the analysis of smFISH images.
  ☆59Updated last year
• drieslab / Giotto
  Spatial omics analysis toolbox
  ☆300Updated this week
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆354Updated last month
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆197Updated 2 months ago
• gustaveroussy / sopa
  Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…
  ☆189Updated last week
• scverse / squidpy
  Spatial Single Cell Analysis in Python
  ☆487Updated this week
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆326Updated 9 months ago
• kharchenkolab / Baysor
  Bayesian Segmentation of Spatial Transcriptomics Data
  ☆171Updated 5 months ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆230Updated this week
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆169Updated last year
• DistributedScience / Distributed-CellProfiler
  Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure.
  ☆41Updated 2 weeks ago
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆206Updated last year
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆363Updated 11 months ago
• broadinstitute / Drop-seq
  Java tools for analyzing Drop-seq data
  ☆127Updated last week
• scverse / spatialdata
  An open and interoperable data framework for spatial omics data
  ☆278Updated this week
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆348Updated 4 months ago
• linnarsson-lab / loompy
  Python implementation of the Loom file format - http://loompy.org
  ☆143Updated 4 months ago
• kharchenkolab / pagoda2
  R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
  ☆229Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆144Updated 5 months ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆234Updated 2 months ago
• theislab / paga
  Mapping out the coarse-grained connectivity structures of complex manifolds.
  ☆215Updated 4 years ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆348Updated 3 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆420Updated last year
• ZhuangLab / MERFISH_analysis
  Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.
  ☆50Updated 3 years ago
• Teichlab / cellphonedb
  ☆354Updated 3 years ago
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆131Updated 6 months ago
• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆193Updated last week
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆331Updated 2 months ago