Alternatives and similar repositories for epiScanpy:

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

• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆161Updated last year
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆143Updated last year
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆160Updated last year
• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆189Updated 2 months ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆158Updated 2 weeks ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆146Updated 4 years ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆197Updated last month
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆137Updated last year
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆170Updated this week
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆152Updated 2 years ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆150Updated this week
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆124Updated last month
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆132Updated this week
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆182Updated 4 years ago
• czbiohub-sf / tabula-muris-senis
  Tabula Muris Senis
  ☆100Updated last year
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆118Updated last year
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆112Updated last week
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆197Updated last year
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆86Updated 2 weeks ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆99Updated last year
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆138Updated last year
• rajewsky-lab / novosparc
  ☆127Updated last year
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆129Updated 2 years ago
• scverse / scanpy_usage
  Scanpy use cases.
  ☆83Updated 4 years ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆199Updated 8 months ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆103Updated 2 months ago
• YosefLab / VISION
  Signature Analysis and Visualization for Single-Cell RNA-seq
  ☆165Updated 10 months ago
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆186Updated 3 weeks ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆157Updated last year
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆163Updated 11 months ago