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
  ☆1,411Updated 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…
  ☆1,498Updated 2 years ago
• satijalab / seurat
  R toolkit for single cell genomics
  ☆2,470Updated this week
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆951Updated this week
• scverse / anndata
  Annotated data.
  ☆636Updated this week
• seandavi / awesome-single-cell
  Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
  ☆3,433Updated 3 weeks ago
• chanzuckerberg / cellxgene
  An interactive explorer for single-cell transcriptomics data
  ☆696Updated this week
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆643Updated last month
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆712Updated last week
• mikelove / awesome-multi-omics
  List of software packages for multi-omics analysis
  ☆818Updated 3 months ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,327Updated last week
• Starlitnightly / omicverse
  A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
  ☆677Updated last week
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆1,016Updated 3 years ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆522Updated 3 weeks ago
• owkin / PyDESeq2
  A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
  ☆659Updated last week
• hemberg-lab / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆676Updated 3 years ago
• crazyhottommy / getting-started-with-genomics-tools-and-resources
  Unix, R and python tools for genomics and data science
  ☆1,290Updated 4 months ago
• OpenGene / fastp
  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
  ☆2,121Updated last week
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,063Updated last week
• hbctraining / Intro-to-scRNAseq
  ☆607Updated 3 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…
  ☆1,379Updated 2 years ago
• hbctraining / scRNA-seq
  ☆571Updated 4 years ago
• YuLab-SMU / clusterProfiler
  A universal enrichment tool for interpreting omics data
  ☆1,101Updated 3 months ago
• sqjin / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
  ☆709Updated last year
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆580Updated 8 months ago
• tanghaibao / goatools
  Python library to handle Gene Ontology (GO) terms
  ☆842Updated last month
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆625Updated 5 months ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆826Updated last year
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆451Updated 4 months ago
• bcbio / bcbio-nextgen
  Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
  ☆1,008Updated 10 months ago