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
  ☆147Updated 10 months ago
• scverse / scanpy_usage
  Scanpy use cases.
  ☆87Updated 5 years ago
• theislab / sfaira
  data and model repository for single-cell data
  ☆135Updated last year
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆176Updated 2 years ago
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆225Updated last week
• rajewsky-lab / novosparc
  ☆131Updated last year
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆168Updated 6 months ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆176Updated last year
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆140Updated last week
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆141Updated 2 years ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆105Updated last year
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆168Updated last year
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆170Updated last week
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆122Updated last month
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆204Updated 7 months ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆150Updated last year
• 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…
  ☆104Updated 5 months ago
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆144Updated 2 months ago
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆175Updated last year
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆113Updated 11 months ago
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆130Updated last year
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆157Updated 4 years ago
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆158Updated last month
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆138Updated 2 years ago
• ShobiStassen / VIA
  trajectory inference
  ☆105Updated 8 months ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 7 months ago
• kharchenkolab / conos
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆215Updated last year
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆113Updated last year
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆111Updated last year
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆92Updated last month