Alternatives and similar repositories for scgen

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

• theislab / scarches
  Reference mapping for single-cell genomics
  ☆383Updated this week
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆384Updated 3 weeks ago
• scverse / pertpy
  Single-cell perturbation analysis
  ☆203Updated this week
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆382Updated 9 months ago
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆218Updated 3 months ago
• openproblems-bio / openproblems
  Formalizing and benchmarking open problems in single-cell genomics
  ☆398Updated last month
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆397Updated last month
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆231Updated last year
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆223Updated last week
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆472Updated last month
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆238Updated this week
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆380Updated last week
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆408Updated this week
• theislab / sc-pert
  Models and datasets for perturbational single-cell omics
  ☆164Updated 3 years ago
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆148Updated 7 months ago
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆229Updated 2 weeks ago
• gao-lab / GLUE
  Graph-linked unified embedding for single-cell multi-omics data integration
  ☆427Updated last month
• KrishnaswamyLab / MAGIC
  MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …
  ☆373Updated last year
• scverse / muon
  muon is a multimodal omics Python framework
  ☆247Updated last month
• Murali-group / Beeline
  BEELINE: evaluation of algorithms for gene regulatory network inference
  ☆194Updated 3 months ago
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆225Updated last week
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆371Updated last month
• broadinstitute / Tangram
  Spatial alignment of single cell transcriptomic data.
  ☆325Updated 3 months ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆204Updated 7 months ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆239Updated last week
• snap-stanford / SATURN
  ☆139Updated last year
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆289Updated 2 months ago
• theislab / paga
  Mapping out the coarse-grained connectivity structures of complex manifolds.
  ☆227Updated 5 years ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆147Updated 10 months ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆542Updated 3 months ago