Alternatives and similar repositories for scib-metrics:

Users that are interested in scib-metrics are comparing it to the libraries listed below

• theislab / scib-reproducibility
  Additional code and analysis from the single-cell integration benchmarking project
  ☆59Updated 2 years ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 5 months ago
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆116Updated 3 weeks ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆63Updated last month
• atarashansky / SCTransformPy
  A python port of the R package SCTransform:
  ☆19Updated 3 years ago
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆110Updated last year
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆96Updated last week
• YosefLab / popV
  ☆71Updated last week
• ma-compbio / SpiceMix
  spatial transcriptome, single cell
  ☆67Updated 2 years ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆50Updated 2 weeks ago
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆164Updated 7 months ago
• Lotfollahi-lab / nichecompass
  End-to-end analysis of spatial multi-omics data
  ☆55Updated this week
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆61Updated 10 months ago
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆66Updated last year
• mossjacob / pyslingshot
  Python implementation of the Slingshot pseudotime algorithm
  ☆59Updated 10 months ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆156Updated 8 months ago
• SONGDONGYUAN1994 / scDesign3
  scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
  ☆90Updated 3 weeks ago
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆103Updated 5 months ago
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆102Updated last year
• bowang-lab / DeepVelo
  ☆47Updated last year
• scverse / pertpy
  Perturbation Analysis in the scverse ecosystem.
  ☆165Updated this week
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆40Updated 3 years ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆69Updated 2 months ago
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆51Updated 8 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆59Updated 9 months ago
• theislab / scTab
  ☆57Updated 6 months ago
• lilab-bcb / harmony-pytorch
  ☆51Updated this week
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆61Updated 6 months ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆129Updated 2 years ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆100Updated last month