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.
  ☆223Updated this week
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆237Updated this week
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆204Updated 6 months ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆147Updated 9 months ago
• scverse / pertpy
  Single-cell perturbation analysis
  ☆201Updated last week
• Teichlab / bbknn
  Batch balanced KNN
  ☆170Updated last year
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆228Updated 2 months ago
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆99Updated 3 months ago
• theislab / sfaira
  data and model repository for single-cell data
  ☆135Updated last year
• scverse / rapids_singlecell
  rapids_singlecell: GPU-accelerated framework for scRNA analysis
  ☆239Updated this week
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆382Updated last month
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆227Updated last year
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆285Updated 2 weeks ago
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆138Updated last week
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆109Updated last week
• slowkow / awesome-vdj
  📚 Tools and databases for analyzing HLA and VDJ genes.
  ☆228Updated 4 months ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆155Updated 4 years ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆220Updated this week
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆289Updated 2 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆354Updated last month
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆376Updated 2 weeks ago
• pachterlab / kb_python
  A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
  ☆167Updated 3 months ago
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆118Updated 3 years ago
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆393Updated last week
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆118Updated last week
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆184Updated 4 years ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆168Updated last week
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆157Updated last week
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆214Updated 2 months ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆176Updated last year