Alternatives and similar repositories for cellxgene

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

• 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
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆451Updated 4 months ago
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆712Updated last week
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆424Updated 5 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆551Updated 2 weeks ago
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆643Updated last month
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆580Updated 8 months ago
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆951Updated this week
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆366Updated 6 months ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆327Updated this week
• Teichlab / cellphonedb
  ☆357Updated 3 years ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆429Updated 2 weeks ago
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆625Updated 5 months ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆409Updated last month
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆426Updated 7 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆498Updated last week
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆427Updated last month
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆365Updated 3 weeks ago
• cole-trapnell-lab / monocle3
  ☆391Updated 2 weeks ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆347Updated 4 months ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆375Updated last month
• owkin / PyDESeq2
  A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
  ☆659Updated last week
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆471Updated last month
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆387Updated 3 weeks ago
• scverse / anndata
  Annotated data.
  ☆636Updated this week
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆289Updated 3 weeks ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆379Updated this week
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆366Updated 6 months ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆482Updated 3 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆748Updated 3 months ago