Alternatives and similar repositories for Tangram

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

• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆357Updated 2 months ago
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆223Updated this week
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆367Updated 3 weeks ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆357Updated 4 months ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆367Updated 3 weeks ago
• scverse / pertpy
  Perturbation Analysis in the scverse ecosystem.
  ☆177Updated this week
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆208Updated 3 months ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆365Updated last week
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆356Updated 4 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆213Updated this week
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆245Updated this week
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆192Updated last week
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆393Updated last week
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆224Updated 4 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆425Updated last year
• QuKunLab / SpatialBenchmarking
  ☆119Updated 2 years ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆170Updated last year
• kaizhang / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆260Updated this week
• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆196Updated this week
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆331Updated 10 months ago
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆387Updated last month
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆197Updated 3 months ago
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆129Updated 3 months ago
• theislab / single-cell-transformer-papers
  ☆315Updated last week
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆201Updated last year
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆411Updated last month
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆296Updated 3 months ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆342Updated 3 months ago
• azizilab / starfysh
  Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology
  ☆118Updated this week
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆453Updated this week