Alternatives and similar repositories for harmonypy

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

• scverse / pertpy
  Single-cell perturbation analysis
  ☆205Updated last week
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆231Updated last week
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆234Updated this week
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆243Updated last week
• Teichlab / bbknn
  Batch balanced KNN
  ☆172Updated 2 years ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆148Updated 10 months ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆252Updated last week
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆225Updated this week
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆388Updated last month
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆220Updated 4 months ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆142Updated 2 years ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆386Updated 3 weeks ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆204Updated last week
• theislab / scgen
  Single cell perturbation prediction
  ☆322Updated 10 months ago
• broadinstitute / Tangram
  Spatial alignment of single cell transcriptomic data.
  ☆331Updated 3 months ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆174Updated last week
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆402Updated last month
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆384Updated 2 weeks ago
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆175Updated last year
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆242Updated last week
• theislab / paga
  Mapping out the coarse-grained connectivity structures of complex manifolds.
  ☆229Updated 5 years ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆380Updated 2 months ago
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆291Updated 3 months ago
• theislab / moscot
  Multi-omic single-cell optimal transport tools
  ☆176Updated this week
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆392Updated 9 months ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆175Updated last year
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆216Updated 2 years ago
• dpeerlab / Palantir
  Single cell trajectory detection
  ☆271Updated 4 months ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆414Updated 2 weeks ago
• theislab / sfaira
  data and model repository for single-cell data
  ☆135Updated last year