Alternatives and similar repositories for bbknn

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

• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆158Updated last month
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆144Updated 5 months ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆101Updated last year
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆163Updated 2 years ago
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆127Updated 2 months ago
• rajewsky-lab / novosparc
  ☆130Updated last year
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆147Updated last year
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆71Updated 3 months ago
• scverse / scanpy_usage
  Scanpy use cases.
  ☆85Updated 4 years ago
• quadbio / Pando
  Multiome GRN inference.
  ☆121Updated last year
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆139Updated last year
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆149Updated 4 years ago
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆137Updated last year
• ShobiStassen / VIA
  trajectory inference
  ☆98Updated 3 months ago
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆132Updated this week
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆174Updated 3 weeks ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆202Updated 9 months ago
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆89Updated last month
• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆194Updated last week
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆117Updated 8 months ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 6 months ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆169Updated last year
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆154Updated this week
• kharchenkolab / conos
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆212Updated last year
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆106Updated 7 months ago
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆157Updated 2 years ago
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆111Updated 6 months ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆163Updated last year
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆113Updated this week
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆169Updated 2 weeks ago