Alternatives and similar repositories for harmonypy

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

• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆207Updated this week
• scverse / pertpy
  Perturbation Analysis in the scverse ecosystem.
  ☆182Updated last week
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆218Updated this week
• Teichlab / bbknn
  Batch balanced KNN
  ☆162Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆144Updated 6 months ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆239Updated 3 months ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆363Updated 5 months ago
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆224Updated last week
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆370Updated last month
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆198Updated 4 months ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆233Updated 2 weeks ago
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆389Updated 2 months ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆159Updated 2 weeks ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆132Updated 2 years ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆172Updated last year
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆227Updated 5 months ago
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆168Updated 10 months ago
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆197Updated this week
• theislab / paga
  Mapping out the coarse-grained connectivity structures of complex manifolds.
  ☆219Updated 5 years ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆375Updated last month
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆343Updated 3 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆333Updated 11 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆215Updated this week
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆129Updated 4 months ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆208Updated 10 months ago
• theislab / sc-pert
  Models and datasets for perturbational single-cell omics
  ☆152Updated 2 years ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆153Updated 4 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆162Updated 2 months ago
• cantinilab / scPRINT
  single cell foundation model for Gene network inference and more
  ☆88Updated this week
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆362Updated 2 months ago