Alternatives and similar repositories for muon

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

• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆238Updated this week
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆242Updated last week
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆204Updated 3 weeks ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆148Updated 11 months ago
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆243Updated 3 weeks ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆174Updated 2 years ago
• scverse / pertpy
  Single-cell perturbation analysis
  ☆212Updated last week
• scverse / rapids_singlecell
  rapids_singlecell: GPU-accelerated framework for scRNA analysis
  ☆261Updated this week
• theislab / sfaira
  data and model repository for single-cell data
  ☆135Updated last year
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆298Updated this week
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆98Updated 2 weeks ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆228Updated this week
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆424Updated last week
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆177Updated last week
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆292Updated 4 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆365Updated 3 months ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆158Updated 4 years ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆387Updated last month
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆241Updated last year
• pachterlab / kb_python
  A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
  ☆177Updated 2 weeks ago
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆142Updated last week
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆223Updated 4 months ago
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆113Updated last week
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆392Updated last month
• slowkow / awesome-vdj
  📚 Tools and databases for analyzing HLA and VDJ genes.
  ☆233Updated last month
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆169Updated 7 months ago
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆159Updated last week
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆178Updated last year
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆384Updated 2 months ago
• mortazavilab / PyWGCNA
  PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
  ☆277Updated 8 months ago