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.
  ☆169Updated 2 years ago
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆143Updated last week
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆188Updated 3 weeks ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆177Updated 2 years ago
• theislab / sfaira
  data and model repository for single-cell data
  ☆136Updated 2 years ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆162Updated 5 years ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆107Updated 2 years ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆180Updated 2 weeks ago
• rajewsky-lab / novosparc
  ☆131Updated 2 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆178Updated 10 months ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆149Updated 3 years ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆182Updated last year
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆206Updated 3 months ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆155Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆81Updated 11 months ago
• ShobiStassen / VIA
  trajectory inference
  ☆105Updated last year
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆140Updated 2 years ago
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆161Updated 2 weeks ago
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆253Updated last week
• scverse / scanpy_usage
  Scanpy use cases.
  ☆90Updated 5 years ago
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆171Updated 3 years ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆245Updated last week
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆114Updated last year
• YosefLab / VISION
  Signature Analysis and Visualization for Single-Cell RNA-seq
  ☆175Updated last year
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆81Updated last year
• calico / solo
  software to detect doublets
  ☆96Updated last year
• tuonglab / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package
  ☆124Updated this week
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆143Updated 2 years ago
• YosefLab / Compass
  In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
  ☆121Updated 3 months ago
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆95Updated 5 months ago