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…
  ☆527Updated last month
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆456Updated 5 months ago
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆424Updated 5 months ago
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆720Updated 2 weeks ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆432Updated 8 months ago
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆648Updated this week
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆559Updated 2 weeks ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆372Updated 7 months ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆395Updated this week
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆418Updated 2 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆345Updated last week
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆473Updated 2 months ago
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆632Updated 6 months ago
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆984Updated 3 weeks ago
• hbctraining / Intro-to-scRNAseq
  ☆612Updated 3 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆434Updated last year
• cole-trapnell-lab / monocle3
  ☆397Updated last month
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆384Updated 3 weeks ago
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆588Updated 8 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆441Updated last month
• owkin / PyDESeq2
  A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
  ☆663Updated this week
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆387Updated 3 weeks ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆483Updated 4 months ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆372Updated last month
• scverse / anndata
  Annotated data.
  ☆643Updated this week
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆499Updated this week
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆377Updated 2 weeks ago
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆426Updated 2 weeks ago
• NVIDIA-Genomics-Research / rapids-single-cell-examples
  Examples of single-cell genomic analysis accelerated with RAPIDS
  ☆340Updated 2 years ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆329Updated this week