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.
  ☆139Updated 2 years ago
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆138Updated last week
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆173Updated 2 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆167Updated last year
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆223Updated this week
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆105Updated last year
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆168Updated last week
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆155Updated 4 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆167Updated 5 months ago
• rajewsky-lab / novosparc
  ☆131Updated last year
• Teichlab / bbknn
  Batch balanced KNN
  ☆170Updated last year
• ShobiStassen / VIA
  trajectory inference
  ☆104Updated 7 months ago
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆130Updated last year
• theislab / sfaira
  data and model repository for single-cell data
  ☆135Updated last year
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆122Updated last week
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆176Updated last year
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆118Updated this week
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆142Updated last month
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆204Updated 6 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆76Updated 7 months ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆150Updated last year
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆90Updated 3 weeks ago
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆138Updated 2 years ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 10 months ago
• scverse / scanpy_usage
  Scanpy use cases.
  ☆86Updated 5 years ago
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆174Updated last year
• quadbio / Pando
  Multiome GRN inference.
  ☆127Updated last year
• KrishnaswamyLab / SingleCellWorkshop
  ☆93Updated 4 years ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆214Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 6 months ago