Alternatives and similar repositories for bbknn

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

• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆144Updated 6 months ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆165Updated 2 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆162Updated 2 months ago
• rajewsky-lab / novosparc
  ☆130Updated last year
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆89Updated last week
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 8 months ago
• scverse / scanpy_usage
  Scanpy use cases.
  ☆85Updated 4 years ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆101Updated last year
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆162Updated last year
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆149Updated last year
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆129Updated 4 months ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆132Updated 2 years ago
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆137Updated last year
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆153Updated 4 years ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆159Updated 2 weeks ago
• campbio / celda
  Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data
  ☆148Updated 4 months ago
• quadbio / Pando
  Multiome GRN inference.
  ☆124Updated last year
• ShobiStassen / VIA
  trajectory inference
  ☆103Updated 4 months ago
• czbiohub-sf / tabula-muris-senis
  Tabula Muris Senis
  ☆103Updated 2 years ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆74Updated 5 months ago
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆136Updated last week
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆150Updated last month
• brianhie / geosketch
  Geometry-preserving random sampling
  ☆87Updated 7 months ago
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆124Updated last year
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆107Updated 9 months ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆172Updated last year
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆118Updated 9 months ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆208Updated 10 months ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆71Updated 4 months ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆147Updated 5 months ago