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
  ☆389Updated last month
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆393Updated 2 months ago
• scverse / pertpy
  Single-cell perturbation analysis
  ☆213Updated last week
• openproblems-bio / openproblems
  Formalizing and benchmarking open problems in single-cell genomics
  ☆412Updated 3 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆228Updated this week
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆241Updated last year
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆407Updated last week
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆226Updated 4 months ago
• theislab / sc-pert
  Models and datasets for perturbational single-cell omics
  ☆167Updated 3 years ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆397Updated 10 months ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆391Updated last week
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆245Updated this week
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆473Updated last week
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆425Updated this week
• KrishnaswamyLab / MAGIC
  MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …
  ☆375Updated last year
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆234Updated 3 weeks ago
• broadinstitute / Tangram
  Spatial alignment of single cell transcriptomic data.
  ☆336Updated 4 months ago
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆292Updated 4 months ago
• gao-lab / GLUE
  Graph-linked unified embedding for single-cell multi-omics data integration
  ☆433Updated last week
• scverse / muon
  muon is a multimodal omics Python framework
  ☆254Updated last week
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆238Updated last week
• Teichlab / bbknn
  Batch balanced KNN
  ☆174Updated 2 years ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆388Updated 2 months ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆205Updated 3 weeks ago
• theislab / paga
  Mapping out the coarse-grained connectivity structures of complex manifolds.
  ☆231Updated 5 years ago
• dpeerlab / Palantir
  Single cell trajectory detection
  ☆273Updated last week
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆242Updated last week
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆148Updated 11 months ago
• snap-stanford / SATURN
  ☆143Updated last year
• YosefLab / scib-metrics
  Accelerated, Python-only, single-cell integration benchmarking metrics
  ☆77Updated last week