Alternatives and similar repositories for SPOTlight

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

• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆167Updated 3 months ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆224Updated last year
• sunduanchen / Scissor
  Scissor package
  ☆243Updated last year
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆183Updated 2 years ago
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆218Updated last month
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆148Updated 3 months ago
• YMa-lab / CARD
  ☆128Updated last year
• mojaveazure / seurat-disk
  Interfaces for HDF5-based Single Cell File Formats
  ☆168Updated 2 years ago
• cellgeni / schard
  reticulate-free single cell format conversion
  ☆197Updated this week
• wu-yc / scMetabolism
  Quantifying metabolism activity at the single-cell resolution
  ☆147Updated 5 months ago
• 10XGenomics / HumanColonCancer_VisiumHD
  Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…
  ☆103Updated 5 months ago
• carmonalab / GeneNMF
  Methods to discover gene programs on single-cell data
  ☆163Updated 2 months ago
• zktuong / ktplots
  Some tools for plotting single-cell data
  ☆176Updated 6 months ago
• carmonalab / UCell
  Gene set scoring for single-cell data
  ☆171Updated last month
• aertslab / SCENICprotocol
  A scalable SCENIC workflow for single-cell gene regulatory network analysis
  ☆168Updated 2 years ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆234Updated 2 years ago
• quadbio / Pando
  Multiome GRN inference.
  ☆131Updated last year
• Sijin-ZhangLab / PanMyeloid
  ☆110Updated 5 years ago
• digitalcytometry / cytotrace2
  CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.
  ☆195Updated last month
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆192Updated this week
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆129Updated last month
• neurorestore / Augur
  Cell type prioritization in single-cell data
  ☆128Updated last year
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆136Updated 9 months ago
• aertslab / AUCell
  AUCell: score single cells with gene regulatory networks
  ☆174Updated last year
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆119Updated last year
• PaulingLiu / ROGUE
  Assessing the purity of single cell population
  ☆137Updated 3 years ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆299Updated 3 months ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆222Updated last year
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆169Updated 8 months ago
• enblacar / SCpubr
  Generate high quality, publication ready visualizations for single cell transcriptomics data.
  ☆212Updated 3 months ago