Alternatives and similar repositories for stLearn

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

• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆263Updated last week
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆415Updated 2 weeks ago
• broadinstitute / Tangram
  Spatial alignment of single cell transcriptomic data.
  ☆352Updated 7 months ago
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆248Updated last week
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆253Updated this week
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆234Updated last week
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆405Updated 5 months ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆404Updated 4 months ago
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆149Updated 2 weeks ago
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆233Updated last month
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆451Updated this week
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆272Updated 2 months ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆182Updated last year
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆149Updated 3 years ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆177Updated 2 years ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆230Updated last year
• gustaveroussy / sopa
  Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…
  ☆261Updated 3 weeks ago
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆135Updated 3 months ago
• scverse / pertpy
  Single-cell perturbation analysis
  ☆283Updated this week
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆180Updated last week
• scverse / rapids_singlecell
  rapids_singlecell: GPU-accelerated framework for scRNA analysis
  ☆296Updated this week
• MarcElosua / SPOTlight
  Spatial Transcriptomics Capture Location Deconvolution
  ☆200Updated 3 months ago
• zcang / COMMOT
  ☆129Updated last year
• azizilab / starfysh
  Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology
  ☆128Updated 8 months ago
• drieslab / Giotto
  Spatial omics analysis toolbox
  ☆359Updated last week
• QuKunLab / SpatialBenchmarking
  ☆129Updated 3 years ago
• YMa-lab / CARD
  ☆129Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆149Updated last year
• LieberInstitute / spatialLIBD
  Code for the spatialLIBD R/Bioconductor package and shiny app
  ☆107Updated 3 weeks ago
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆186Updated last week