Alternatives and similar repositories for scanpy:

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

• scverse / anndata
  Annotated data.
  ☆592Updated this week
• scverse / scvi-tools
  Deep probabilistic analysis of single-cell and spatial omics data
  ☆1,307Updated this week
• theislab / single-cell-tutorial
  Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…
  ☆1,432Updated 2 years ago
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆819Updated this week
• satijalab / seurat
  R toolkit for single cell genomics
  ☆2,343Updated this week
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆653Updated last month
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆587Updated last month
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆971Updated 3 years ago
• chanzuckerberg / cellxgene
  An interactive explorer for single-cell transcriptomics data
  ☆654Updated last month
• hbctraining / scRNA-seq
  ☆548Updated 3 years ago
• hemberg-lab / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆674Updated 2 years ago
• seandavi / awesome-single-cell
  Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
  ☆3,275Updated last month
• YuLab-SMU / clusterProfiler
  A universal enrichment tool for interpreting omics data
  ☆1,051Updated last month
• mikelove / awesome-multi-omics
  List of software packages for multi-omics analysis
  ☆749Updated 8 months ago
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆541Updated 2 months ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆463Updated 9 months ago
• sqjin / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
  ☆657Updated last year
• hbctraining / scRNA-seq_online
  ☆544Updated this week
• crazyhottommy / scRNAseq-analysis-notes
  scRNAseq analysis notes from Ming Tang
  ☆663Updated last month
• Starlitnightly / omicverse
  A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
  ☆538Updated 3 weeks ago
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆959Updated this week
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆414Updated 2 weeks ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆422Updated last month
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆759Updated 5 months ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆379Updated last month
• cole-trapnell-lab / monocle3
  ☆360Updated last week
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆588Updated 2 months ago
• openproblems-bio / openproblems
  Formalizing and benchmarking open problems in single-cell genomics
  ☆323Updated last month
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆719Updated last month
• scverse / squidpy
  Spatial Single Cell Analysis in Python
  ☆454Updated this week