Alternatives and similar repositories for cellxgene

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

• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆478Updated last month
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆437Updated this week
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆563Updated 5 months ago
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆677Updated this week
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆760Updated 2 weeks ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆454Updated last year
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆615Updated 2 months ago
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆1,075Updated last month
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆598Updated last month
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆403Updated 11 months ago
• owkin / PyDESeq2
  A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
  ☆708Updated this week
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆448Updated 6 months ago
• scverse / scvi-tools
  Deep probabilistic analysis of single-cell and spatial omics data
  ☆1,514Updated this week
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆436Updated 2 weeks ago
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆430Updated last month
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆395Updated last week
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆645Updated last month
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆394Updated 3 months ago
• hbctraining / Intro-to-scRNAseq
  ☆635Updated last week
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆333Updated this week
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆421Updated 4 months ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆486Updated 6 months ago
• Teichlab / cellphonedb
  ☆359Updated 4 years ago
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆477Updated last week
• cole-trapnell-lab / monocle3
  ☆424Updated 2 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆502Updated 2 months ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆401Updated this week
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆303Updated last month
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆513Updated 8 months ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆399Updated this week