Alternatives and similar repositories for scanpy

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

• scverse / scvi-tools
  Deep probabilistic analysis of single-cell and spatial omics data
  ☆1,427Updated last 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…
  ☆1,505Updated 2 years ago
• satijalab / seurat
  R toolkit for single cell genomics
  ☆2,500Updated last week
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆1,000Updated last month
• seandavi / awesome-single-cell
  Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
  ☆3,465Updated this week
• scverse / anndata
  Annotated data.
  ☆649Updated this week
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆727Updated 2 weeks ago
• hemberg-lab / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆675Updated 3 years ago
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆650Updated this week
• chanzuckerberg / cellxgene
  An interactive explorer for single-cell transcriptomics data
  ☆710Updated last week
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆596Updated 9 months ago
• hbctraining / scRNA-seq
  ☆575Updated 4 years ago
• hbctraining / Intro-to-scRNAseq
  ☆618Updated 4 months ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆461Updated 6 months ago
• mikelove / awesome-multi-omics
  List of software packages for multi-omics analysis
  ☆828Updated 4 months ago
• sqjin / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
  ☆725Updated last year
• Starlitnightly / omicverse
  A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
  ☆713Updated this week
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆533Updated 2 months ago
• YuLab-SMU / clusterProfiler
  A universal enrichment tool for interpreting omics data
  ☆1,114Updated 4 months ago
• owkin / PyDESeq2
  A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
  ☆668Updated this week
• crazyhottommy / scRNAseq-analysis-notes
  scRNAseq analysis notes from Ming Tang
  ☆733Updated 8 months ago
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆1,030Updated 3 years ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆435Updated 9 months ago
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,089Updated last week
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆633Updated 6 months ago
• griffithlab / rnaseq_tutorial
  Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis inclu…
  ☆1,382Updated 2 years ago
• tanghaibao / goatools
  Python library to handle Gene Ontology (GO) terms
  ☆851Updated 3 months ago
• bowang-lab / scGPT
  ☆1,306Updated last month
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆835Updated last year
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆815Updated last year