Alternatives and similar repositories for scanpy_usage

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

• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆105Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆145Updated 8 months ago
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆138Updated this week
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆157Updated 3 weeks ago
• rajewsky-lab / novosparc
  ☆131Updated last year
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆149Updated last year
• AllonKleinLab / SPRING_dev
  ☆70Updated 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…
  ☆101Updated 4 months ago
• JonathanShor / DoubletDetection
  Doublet detection in single-cell RNA-seq data.
  ☆92Updated 6 months ago
• AllonMKlein / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆85Updated 6 years ago
• miaozhun / DEsingle
  Homepage: https://miaozhun.github.io/DEsingle. Bioconductor page: https://bioconductor.org/packages/DEsingle.
  ☆31Updated 2 years ago
• velocyto-team / velocyto-notebooks
  ☆55Updated 7 years ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆169Updated last year
• mohuangx / SAVER
  Single-cell RNA-seq Gene Expression Recovery
  ☆111Updated 9 months ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆167Updated last year
• AllonKleinLab / SPRING
  ☆69Updated 7 years ago
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆118Updated 2 weeks ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated 4 months ago
• Novartis / cellxgene-gateway
  Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cel…
  ☆65Updated last year
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆76Updated 7 months ago
• KrishnaswamyLab / SingleCellWorkshop
  ☆93Updated 4 years ago
• theislab / sfaira
  data and model repository for single-cell data
  ☆135Updated last year
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆138Updated 2 years ago
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆112Updated 9 months ago
• Teichlab / embl-single-cell-course-2016
  Material for lecture at the EMBL Single Cell Course 2016
  ☆47Updated 9 years ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆121Updated last week
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆94Updated 6 years ago
• calico / solo
  software to detect doublets
  ☆94Updated 7 months ago
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆141Updated last year
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆175Updated last year