Alternatives and similar repositories for openproblems-v2

Users that are interested in openproblems-v2 are comparing it to the libraries listed below

• theislab / DRVI
  Unsupervised Deep Disentangled Representation of Single-Cell Omics
  ☆46Updated last week
• YosefLab / scib-metrics
  Accelerated, Python-only, single-cell integration benchmarking metrics
  ☆63Updated this week
• SONGDONGYUAN1994 / scDesign3
  scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
  ☆100Updated 5 months ago
• theislab / scib-reproducibility
  Additional code and analysis from the single-cell integration benchmarking project
  ☆67Updated 2 years ago
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆172Updated last year
• Lotfollahi-lab / nichecompass
  End-to-end analysis of spatial multi-omics data
  ☆89Updated this week
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated 3 months ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆137Updated 2 years ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 5 months ago
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆105Updated last week
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 9 months ago
• nitzanlab / biolord
  ☆80Updated 11 months ago
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆113Updated last year
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆131Updated 5 months ago
• lilab-bcb / harmony-pytorch
  ☆55Updated 2 months ago
• shuxiaoc / maxfuse
  ☆55Updated last year
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆165Updated 4 months ago
• simonwm / tacco
  TACCO: Transfer of Annotations to Cells and their COmbinations
  ☆52Updated last year
• ma-compbio / SpiceMix
  spatial transcriptome, single cell
  ☆68Updated 2 years ago
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆70Updated last year
• cantinilab / scPRINT
  single cell foundation model for Gene network inference and more
  ☆96Updated last week
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆90Updated this week
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆63Updated last week
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆121Updated 3 weeks ago
• theislab / sfaira
  data and model repository for single-cell data
  ☆135Updated last year
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆110Updated 10 months ago
• theislab / scTab
  ☆59Updated 10 months ago
• mossjacob / pyslingshot
  Python implementation of the Slingshot pseudotime algorithm
  ☆61Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆145Updated 8 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆75Updated 6 months ago