Alternatives and similar repositories for epiScanpy

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

• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆147Updated 2 years ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆160Updated 5 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆169Updated last year
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆248Updated this week
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆143Updated 3 weeks ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆176Updated 2 years ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆185Updated 2 years ago
• theislab / sfaira
  data and model repository for single-cell data
  ☆136Updated 2 years ago
• rajewsky-lab / novosparc
  ☆131Updated 2 years ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆206Updated 2 months ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆179Updated 3 weeks ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆179Updated last year
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆107Updated 2 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆175Updated 9 months ago
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆93Updated 4 months ago
• czbiohub-sf / tabula-muris-senis
  Tabula Muris Senis
  ☆107Updated 2 years ago
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆169Updated 3 years ago
• scverse / scanpy_usage
  Scanpy use cases.
  ☆88Updated 5 years ago
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆152Updated 5 months ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆153Updated last year
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆122Updated this week
• calico / solo
  software to detect doublets
  ☆95Updated last year
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆161Updated 2 months ago
• ShobiStassen / VIA
  trajectory inference
  ☆105Updated 11 months ago
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆139Updated 2 years ago
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆141Updated 2 years ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆243Updated last week
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆114Updated last year
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆184Updated 5 years ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆80Updated 11 months ago