https://github.com/adeschen/signatureheatmap
R package to create heatmaps using signature gene list and transcriptomic data
https://github.com/adeschen/signatureheatmap
classification gene-list gene-signature heatmap heatmap-visualization r rna-seq-data
Last synced: about 1 year ago
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R package to create heatmaps using signature gene list and transcriptomic data
- Host: GitHub
- URL: https://github.com/adeschen/signatureheatmap
- Owner: adeschen
- Created: 2022-11-04T17:05:05.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2023-03-14T02:40:06.000Z (about 3 years ago)
- Last Synced: 2023-09-02T20:43:10.753Z (almost 3 years ago)
- Topics: classification, gene-list, gene-signature, heatmap, heatmap-visualization, r, rna-seq-data
- Language: R
- Homepage: https://adeschen.github.io/SignatureHeatmap/
- Size: 1.94 MB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
[](https://github.com/adeschen/SignatureHeatmap/actions/workflows/check-bioc.yaml)
[](https://codecov.io/gh/adeschen/SignatureHeatmap)
[](https://opensource.org/licenses/Artistic-2.0)
# SignatureHeatmap
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](http://ca.linkedin.com/in/astriddeschenes "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.
## Documentation ##
[SignatureHeatmap Website](https://adeschen.github.io/SignatureHeatmap/)
[SignatureHeatmap Get Started](https://adeschen.github.io/SignatureHeatmap/articles/SignatureHeatmap.html)
## Installation ##
To install the latest version accessible using the [devtools](https://cran.r-project.org/web/packages/devtools/index.html)
package:
## Load required package
library(devtools)
## Install the latest version of SignatureHeatmap
devtools::install_github('adeschen/SignatureHeatmap')
## Maintainer
[Astrid Deschênes](https://github.com/adeschen/ "Astrid Deschênes")
## Bugs/Feature requests ##
[Please contact us](https://github.com/adeschen/SignatureHeatmap/issues) for bug fixes or with feature requests.
Thanks!