Seqtometry

This is an R package for Seqtometry analysis of single cell data by scoring with signatures (gene sets). For additional details regarding the algorithmic details and applications of this method, please see the original Seqtometry publication:

Kousnetsov et al., Single-cell sequencing analysis within biologically relevant dimensions, Cell Systems (2024)

Graphical abstract

Installation

Stable version

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("Seqtometry")

Developmental version

if (!require("remotes", quietly = TRUE))
  install.packages("remotes")

remotes::install_github("HawigerLab/Seqtometry")

[!NOTE] For the accompanying GUI prototype, please see the SeqtometryGUI repository.

Quickstart

Please see the vignette for basic usage. For more detailed protocols involving step-by-step instructions for more advanced workflows, please see the following publication:

Kousnetsov and Hawiger, Analysis of single cell sequencing data by Seqtometry, STAR Protocols (2024)