The SignatureHeatmap package enables signature classification of tumor samples by generating heatmaps using transcriptomic data.
At the moment, three different lists of signature genes are available in the SignatureHeatmap package:
- the original list of basal/classical genes from Moffitt et al. 2015 for pancreatic ductal adenocarcinoma (PDAC) tissue samples
- the updated list of basal/classical genes for PDAC tissue samples from Miyabayashi et al. 2020
- the list of basal/classical genes from Tiriac et al. 2018 that has been developed for PDAC organoids
Authors
Astrid Deschênes, Daniel King and David A. Tuveson
Citation
If you use this package for a publication, we would ask you to cite the following:
Deschênes A, King D and Tuveson DA. SignatureHeatmap: Heatmap using signature gene list and RNA-seq expression data. R package version 0.0.3, https://adeschen.github.io/SignatureHeatmap/
You can also replace the latest by the Research Resource Identifier (RRID), as example:
SignatureHeatmap version 0.0.4, RRID: SCR_022949
If you use one of the available signature gene list, the appropriate paper should be referenced.
For Moffitt et al. 2015
Moffitt RA, Marayati R, Flate EL et al. Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma. Nat Genet. 2015 Oct;47(10):1168-78. doi: 10.1038/ng.3398. Epub 2015 Sep 7. PMID: 26343385; PMCID: PMC4912058.
For Tiriac et al. 2018
Tiriac H, Belleau P, Engle DD et al. Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer. Cancer Discov. 2018 Sep;8(9):1112-1129. doi: 10.1158/2159-8290.CD-18-0349. Epub 2018 May 31. PMID: 29853643; PMCID: PMC6125219.
For Miyabayashi et al. 2020
Miyabayashi K, Baker LA, Deschênes A et al. Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes. Cancer Discov. 2020 Oct;10(10):1566-1589. doi: 10.1158/2159-8290.CD-20-0133. Epub 2020 Jul 23. PMID: 32703770; PMCID: PMC7664990.
Installation
To install the latest version accessible using the devtools package:
## Load required package
library(devtools)
## Install the latest version of SignatureHeatmap
devtools::install_github('adeschen/SignatureHeatmap')
