scverse / muon

Related projects ⓘ

Alternatives and complementary repositories for muon

• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆166Updated 2 months ago
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆166Updated 2 months ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆220Updated this week
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆296Updated 5 months ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆193Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆141Updated this week
• kaizhang / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆231Updated 3 weeks ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆303Updated last month
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆335Updated 3 weeks ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆297Updated 4 months ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆137Updated this week
• slowkow / awesome-vdj
  📚 Tools and databases for analyzing HLA and VDJ genes.
  ☆210Updated 6 months ago
• chanzuckerberg / cellxgene-census
  CZ CELLxGENE Discover Census
  ☆86Updated this week
• Teichlab / bbknn
  Batch balanced KNN
  ☆149Updated last year
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆177Updated 3 years ago
• pachterlab / kb_python
  A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
  ☆154Updated last month
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆170Updated 2 months ago
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆186Updated 2 months ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆133Updated 8 months ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆147Updated 4 months ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆252Updated this week
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆138Updated 3 years ago
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆212Updated 3 months ago
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆168Updated this week
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆306Updated last year
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆182Updated 3 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆188Updated this week
• theislab / sfaira
  data and model repository for single-cell data
  ☆135Updated 11 months ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆154Updated 9 months ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆145Updated 6 months ago