signifinder Workflow: Bulk, Single-cell and Spatial Transcriptomics

This repository contains the scripts for data processing, signature computation and figure generation using bulk, single-cell (SC) and spatial transcriptomics (ST) RNA-Seq data, reported at https://www.biorxiv.org/content/10.1101/2023.03.07.530940v1.

A single .Rmd file is provided for each dataset analysis.

The spatial transcriptomic dataset “Human Breast Cancer: Ductal Carcinoma In Situ, Invasive Carcinoma (FFPE)”, from the 10x Genomics Visium Spatial Gene Expression data (https://www.10xgenomics.com), is already provided in the Data folder as a SpatialExperiment. The object already includes the spot annotation of the histology image, performed by an expert anatomopathologist.

Required Packages

The signifinder package can be installed from Bioconductor:

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

BiocManager::install("signifinder")

Further, to run the workflows, the curatedTCGAData, EDASeq, GEOquery, ggpubr, ggspavis, grid, NbClust, org.Hs.eg.db, RColorBrewer, scater, scone, TMExplorer R packages are required.

Documentation and Contacts

Further details on how to use signifinder are available in the vignette, that includes examples and documentation.

For any problems in using signifinder, please write to stefania.pirrotta@phd.unipd.it.