Alternatives and similar repositories for cellxgene

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

• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆440Updated last month
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆687Updated 3 weeks ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆567Updated 6 months ago
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆768Updated this week
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆601Updated last month
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆482Updated 2 weeks ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆443Updated this week
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆456Updated last year
• Teichlab / cellphonedb
  ☆358Updated 4 years ago
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆617Updated 3 months ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆455Updated 7 months ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆405Updated last year
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆335Updated last week
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆646Updated last month
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆435Updated last week
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆398Updated last month
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆488Updated 7 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆513Updated this week
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆451Updated last year
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆369Updated 5 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆516Updated 3 months ago
• cole-trapnell-lab / monocle3
  ☆429Updated this week
• scverse / PyDESeq2
  A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
  ☆711Updated 2 weeks ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆397Updated 4 months ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆396Updated last month
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆1,095Updated 3 weeks ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆517Updated 9 months ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆400Updated 3 months ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆442Updated 10 months ago
• hbctraining / scRNA-seq
  ☆598Updated 4 years ago