Alternatives and similar repositories for ncem:

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

• ma-compbio / SpiceMix
  spatial transcriptome, single cell
  ☆67Updated last year
• theislab / graphcompass
  GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems
  ☆36Updated last month
• YosefLab / scib-metrics
  Accelerated, Python-only, single-cell integration benchmarking metrics
  ☆54Updated this week
• theislab / moscot
  Multi-omic single-cell optimal transport tools
  ☆131Updated this week
• dpeerlab / ENVI
  ☆43Updated 3 months ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆109Updated 3 months ago
• scverse / pertpy
  Perturbation Analysis in the scverse ecosystem.
  ☆154Updated this week
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆109Updated last year
• raphael-group / paste
  Probabilistic Alignment of Spatial Transcriptomics Experiments
  ☆84Updated last year
• snap-stanford / stellar
  ☆64Updated 2 years ago
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆95Updated this week
• KrishnaswamyLab / MELD
  Quantifying experimental perturbations at single cell resolution
  ☆106Updated 4 months ago
• YangLabHKUST / SpatialScope
  A unified approach for integrating spatial and single-cell transcriptomics data by leveraging deep generative models
  ☆58Updated 8 months ago
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆105Updated last week
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆71Updated last year
• zcang / SpaOTsc
  ☆45Updated 2 years ago
• theislab / scib-reproducibility
  Additional code and analysis from the single-cell integration benchmarking project
  ☆56Updated 2 years ago
• hui2000ji / scETM
  A generative topic model that facilitates integrative analysis of large-scale single-cell RNA sequencing data.
  ☆49Updated 3 years ago
• scverse / scvi-tutorials
  Notebooks used in scvi-tools tutorials
  ☆51Updated this week
• MICS-Lab / novae
  Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…
  ☆30Updated this week
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆52Updated 8 months ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆39Updated 3 years ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆85Updated 2 weeks ago
• wukevin / babel
  Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
  ☆39Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆62Updated last year
• Lotfollahi-lab / nichecompass
  End-to-end analysis of spatial multi-omics data
  ☆39Updated this week
• CaiGroup / seqFISH-PLUS
  ☆48Updated 3 years ago
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆112Updated last week
• scverse / pytometry
  Flow & mass cytometry analytics.
  ☆43Updated this week
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆101Updated 4 months ago