Alternatives and similar repositories for ncem:

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

• theislab / graphcompass
  GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems
  ☆34Updated this week
• ma-compbio / SpiceMix
  spatial transcriptome, single cell
  ☆66Updated last year
• YosefLab / scib-metrics
  Accelerated, Python-only, single-cell integration benchmarking metrics
  ☆53Updated this week
• dpeerlab / ENVI
  ☆43Updated 3 months ago
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆110Updated 4 months ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆108Updated 2 months ago
• scverse / pertpy
  Perturbation Analysis in the scverse ecosystem.
  ☆148Updated this week
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆101Updated 3 weeks ago
• nitzanlab / biolord
  ☆71Updated 5 months ago
• bowang-lab / DeepVelo
  ☆46Updated 11 months ago
• zcang / SpaOTsc
  ☆45Updated 2 years ago
• raphael-group / paste
  Probabilistic Alignment of Spatial Transcriptomics Experiments
  ☆83Updated last year
• theislab / moscot
  Multi-omic single-cell optimal transport tools
  ☆119Updated this week
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆39Updated 3 years ago
• hui2000ji / scETM
  A generative topic model that facilitates integrative analysis of large-scale single-cell RNA sequencing data.
  ☆49Updated 3 years ago
• cantinilab / scPRINT
  single cell foundation model for Gene network inference and more
  ☆40Updated this week
• Lotfollahi-lab / nichecompass
  End-to-end analysis of spatial multi-omics data
  ☆39Updated last week
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆108Updated 11 months ago
• theislab / scib-reproducibility
  Additional code and analysis from the single-cell integration benchmarking project
  ☆56Updated 2 years ago
• theislab / prophet
  ☆27Updated 3 weeks ago
• snap-stanford / SATURN
  ☆111Updated 6 months ago
• YangLabHKUST / SpatialScope
  A unified approach for integrating spatial and single-cell transcriptomics data by leveraging deep generative models
  ☆58Updated 7 months ago
• CaiGroup / seqFISH-PLUS
  ☆48Updated 3 years ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆112Updated 4 months ago
• MICS-Lab / novae
  Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…
  ☆29Updated this week
• klarman-cell-observatory / scPhere
  ☆98Updated last year
• azizilab / starfysh
  Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology
  ☆108Updated 4 months ago
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆91Updated this week
• mossjacob / pyslingshot
  Python implementation of the Slingshot pseudotime algorithm
  ☆55Updated 8 months ago
• welch-lab / VeloVAE
  Deep Generative Modeling of RNA Velocity
  ☆35Updated 2 months ago