Alternatives and similar repositories for SPOTlight

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

• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆213Updated last year
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆154Updated 2 weeks ago
• sunduanchen / Scissor
  Scissor package
  ☆231Updated last year
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆205Updated 3 weeks ago
• cellgeni / schard
  reticulate-free single cell format conversion
  ☆182Updated last month
• wu-yc / scMetabolism
  Quantifying metabolism activity at the single-cell resolution
  ☆138Updated 2 months ago
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆173Updated 2 years ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆231Updated 2 years ago
• carmonalab / GeneNMF
  Methods to discover gene programs on single-cell data
  ☆142Updated last month
• digitalcytometry / cytotrace2
  CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.
  ☆164Updated 5 months ago
• zktuong / ktplots
  Some tools for plotting single-cell data
  ☆174Updated 3 months ago
• quadbio / Pando
  Multiome GRN inference.
  ☆126Updated last year
• carmonalab / UCell
  Gene set scoring for single-cell data
  ☆159Updated 3 months ago
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆119Updated 2 weeks ago
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆133Updated 6 months ago
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆183Updated this week
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆166Updated last year
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆141Updated 3 weeks ago
• enblacar / SCpubr
  Generate high quality, publication ready visualizations for single cell transcriptomics data.
  ☆206Updated 3 weeks ago
• YMa-lab / CARD
  ☆123Updated last year
• neurorestore / Augur
  Cell type prioritization in single-cell data
  ☆124Updated 10 months ago
• Sijin-ZhangLab / PanMyeloid
  ☆106Updated 4 years ago
• navinlabcode / CellTrek
  ☆125Updated 3 years ago
• JiekaiLab / scDIOR
  scDIOR: Single cell data IO softwaRe
  ☆145Updated 3 years ago
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆118Updated 11 months ago
• 10XGenomics / HumanColonCancer_VisiumHD
  Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…
  ☆94Updated 2 months ago
• chuiqin / irGSEA
  The integration of single cell rank-based gene set enrichment analysis
  ☆130Updated last month
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆164Updated 2 years ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆210Updated last year
• mojaveazure / seurat-disk
  Interfaces for HDF5-based Single Cell File Formats
  ☆166Updated last year