Alternatives and similar repositories for scDesign3

Users that are interested in scDesign3 are comparing it to the libraries listed below

• Durenlab / LINGER
  ☆114Updated 4 months ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆141Updated 2 years ago
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆70Updated last year
• theislab / scib-reproducibility
  Additional code and analysis from the single-cell integration benchmarking project
  ☆67Updated 2 years ago
• lanagarmire / Asgard
  ☆44Updated last year
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆111Updated 11 months ago
• saezlab / visium_heart
  Spatial transcriptomics of heart tissue
  ☆95Updated last year
• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆90Updated 9 months ago
• bowang-lab / DeepVelo
  ☆46Updated last year
• 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
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated 5 months ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆122Updated 3 weeks ago
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆111Updated 6 months ago
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆111Updated last year
• SchubertLab / mvTCR
  ☆54Updated 11 months ago
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆65Updated last year
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆130Updated last year
• YosefLab / popV
  ☆83Updated this week
• settylab / Mellon
  Non-parametric density inference for single-cell analysis.
  ☆72Updated 4 months ago
• Lotfollahi-lab / nichecompass
  End-to-end analysis of spatial multi-omics data
  ☆93Updated last month
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆132Updated 7 months ago
• ZhangLabGT / scMultiSim
  A simulator for single cell multi-omics and spatial omics data that provides ground truth to benchmark a wide range of methods.
  ☆61Updated last week
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆65Updated last month
• madilabcode / scNET
  ☆53Updated last week
• omnideconv / omnideconv
  Unified access to several second-generation deconvolution methods
  ☆78Updated last month
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆77Updated 8 months ago
• multitalk / awesome-cell-cell-communication
  Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics
  ☆54Updated 3 months ago
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆175Updated last year
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆148Updated 7 months ago
• andreariba / DeepCycle
  Cell cycle inference in single-cell RNA-seq
  ☆50Updated 2 years ago