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
  ☆142Updated 2 months ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆154Updated 8 months ago
• aertslab / arboreto
  A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
  ☆56Updated 10 months ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆156Updated last year
• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆181Updated 3 weeks ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆99Updated last year
• scverse / scanpy_usage
  Scanpy use cases.
  ☆82Updated 4 years ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆145Updated last week
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆114Updated last year
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆142Updated last year
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆159Updated 9 months ago
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆112Updated this week
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆113Updated 6 months ago
• theislab / sfaira
  data and model repository for single-cell data
  ☆136Updated last year
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆160Updated last year
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆83Updated 5 months ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆62Updated 2 weeks ago
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆135Updated last year
• rajewsky-lab / novosparc
  ☆127Updated last year
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆101Updated 5 months ago
• KrishnaswamyLab / SingleCellWorkshop
  ☆91Updated 4 years ago
• brianhie / geosketch
  Geometry-preserving random sampling
  ☆79Updated 4 months ago
• kharchenkolab / conos
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆204Updated last year
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆109Updated 4 months ago
• calico / solo
  software to detect doublets
  ☆90Updated 2 months ago
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆129Updated 2 years ago
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆132Updated last week
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆135Updated 10 months ago
• parashardhapola / scarf
  Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…
  ☆99Updated last month
• quadbio / Pando
  Multiome GRN inference.
  ☆119Updated 10 months ago