scverse / scanpy

Related projects ⓘ

Alternatives and complementary repositories for scanpy

• scverse / scvi-tools
  Deep probabilistic analysis of single-cell and spatial omics data
  ☆1,252Updated this week
• scverse / anndata
  Annotated data.
  ☆579Updated 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…
  ☆1,398Updated last year
• satijalab / seurat
  R toolkit for single cell genomics
  ☆2,299Updated 3 weeks ago
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆782Updated 2 weeks ago
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆635Updated this week
• chanzuckerberg / cellxgene
  An interactive explorer for single-cell transcriptomics data
  ☆634Updated this week
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆418Updated last month
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆569Updated last week
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆444Updated 7 months ago
• hemberg-lab / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆673Updated 2 years ago
• openproblems-bio / openproblems
  Formalizing and benchmarking open problems in single-cell genomics
  ☆321Updated this week
• hbctraining / scRNA-seq
  ☆539Updated 3 years ago
• scverse / squidpy
  Spatial Single Cell Analysis in Python
  ☆440Updated this week
• seandavi / awesome-single-cell
  Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
  ☆3,227Updated last week
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆421Updated 3 weeks ago
• mikelove / awesome-multi-omics
  List of software packages for multi-omics analysis
  ☆735Updated 7 months ago
• owkin / PyDESeq2
  A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
  ☆590Updated this week
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆529Updated last week
• hbctraining / scRNA-seq_online
  ☆527Updated 3 weeks ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆364Updated this week
• crazyhottommy / scRNAseq-analysis-notes
  scRNAseq analysis notes from Ming Tang
  ☆648Updated last month
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆408Updated 3 weeks ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆416Updated 6 months ago
• cole-trapnell-lab / monocle3
  ☆344Updated 2 weeks ago
• Starlitnightly / omicverse
  A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
  ☆473Updated this week
• sqjin / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
  ☆640Updated 10 months ago
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆941Updated 3 years ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆335Updated last month
• OpenGene / fastp
  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
  ☆1,934Updated 2 weeks ago