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
  ☆101Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆144Updated 6 months ago
• AllonMKlein / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆85Updated 5 years ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆148Updated last year
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆109Updated last month
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆114Updated last week
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆170Updated last year
• hemberg-lab / scmap
  A tool for unsupervised projection of single cell RNA-seq data
  ☆96Updated 4 years ago
• timoast / sinto
  Tools for single-cell data processing
  ☆124Updated last year
• rajewsky-lab / novosparc
  ☆130Updated last year
• Teichlab / embl-single-cell-course-2016
  Material for lecture at the EMBL Single Cell Course 2016
  ☆47Updated 9 years ago
• rnakato / ShortCake
  A docker image for single-cell analysis
  ☆88Updated 4 months ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆140Updated 3 years ago
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆160Updated 2 months ago
• AllonKleinLab / SPRING_dev
  ☆69Updated last year
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆148Updated last week
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated last month
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆162Updated last year
• jfnavarro / st_pipeline
  ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …
  ☆82Updated 3 months ago
• crazyhottommy / scclusteval
  Single Cell Cluster Evaluation
  ☆94Updated 3 years ago
• MarioniLab / EmbryoTimecourse2018
  Data and analysis scripts for our Embryo Timecourse paper.
  ☆68Updated 5 years ago
• GregorySchwartz / too-many-cells
  Cluster single cells and analyze cell clade relationships with colorful visualizations.
  ☆112Updated 7 months ago
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆86Updated 11 months ago
• phbradley / conga
  Clonotype Neighbor Graph Analysis
  ☆89Updated 2 months ago
• bioinfo-ibms-pumc / SCSA
  SCSA: cell type annotation for single-cell RNA-seq data
  ☆90Updated 2 years ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆151Updated 4 years ago
• SpatialTranscriptomicsResearch / st_pipeline
  ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …
  ☆83Updated 4 years ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated 2 years ago
• ggjlab / HCL
  Tools used in Human Cell Landscape(HCL)
  ☆54Updated 4 years ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆73Updated 4 months ago