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.
  ☆241Updated 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.
  ☆205Updated last month
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆247Updated last week
• scverse / pertpy
  Single-cell perturbation analysis
  ☆217Updated last week
• Teichlab / bbknn
  Batch balanced KNN
  ☆176Updated 2 years ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆149Updated last year
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆102Updated last month
• scverse / rapids_singlecell
  rapids_singlecell: GPU-accelerated framework for scRNA analysis
  ☆279Updated this week
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆393Updated this week
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆242Updated last year
• theislab / sfaira
  data and model repository for single-cell data
  ☆136Updated last year
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆301Updated last week
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆395Updated 2 months ago
• pachterlab / kb_python
  A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
  ☆182Updated last month
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆229Updated this week
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆431Updated last week
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆161Updated 4 years ago
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆114Updated last week
• theislab / paga
  Mapping out the coarse-grained connectivity structures of complex manifolds.
  ☆231Updated 5 years ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆180Updated last week
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆227Updated 5 months ago
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆294Updated 4 months ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆176Updated last year
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆366Updated 4 months ago
• slowkow / awesome-vdj
  📚 Tools and databases for analyzing HLA and VDJ genes.
  ☆233Updated 2 months ago
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆409Updated 3 weeks ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆184Updated 5 years ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆401Updated 10 months ago
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆180Updated last year