Alternatives and similar repositories for pertpy

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

• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆233Updated last month
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆263Updated last week
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆164Updated 11 months ago
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆253Updated this week
• theislab / moscot
  Multi-omic single-cell optimal transport tools
  ☆185Updated last week
• theislab / sc-pert
  Models and datasets for perturbational single-cell omics
  ☆172Updated 3 years ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆397Updated 2 months ago
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆248Updated this week
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆186Updated this week
• YosefLab / scib-metrics
  Accelerated, Python-only, single-cell integration benchmarking metrics
  ☆85Updated last week
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆404Updated 4 months ago
• openproblems-bio / openproblems
  Formalizing and benchmarking open problems in single-cell genomics
  ☆420Updated 2 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆234Updated last week
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆238Updated 3 weeks ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆262Updated 2 weeks ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆149Updated 3 years ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆413Updated this week
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆149Updated last year
• ZhangLabGT / scMultiSim
  A simulator for single cell multi-omics and spatial omics data that provides ground truth to benchmark a wide range of methods.
  ☆69Updated 3 months ago
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆115Updated 3 weeks ago
• snap-stanford / SATURN
  ☆155Updated last year
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆415Updated 2 weeks ago
• scverse / rapids_singlecell
  rapids_singlecell: GPU-accelerated framework for scRNA analysis
  ☆296Updated this week
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆206Updated 3 months ago
• nitzanlab / biolord
  ☆90Updated last year
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆179Updated last week
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆413Updated last week
• SONGDONGYUAN1994 / scDesign3
  scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
  ☆113Updated 4 months ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆177Updated 2 years ago
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆308Updated this week