Signatureheatmap
| Project Name | Stars | Downloads | Repos Using This | Packages Using This | Most Recent Commit | Total Releases | Latest Release | Open Issues | License | Language |
|---|---|---|---|---|---|---|---|---|---|---|
| Covid Cxnet | 35 | 2 years ago | 4 | mit | Jupyter Notebook | |||||
| COVID-CXNet: Diagnosing COVID-19 in Frontal Chest X-ray Images using Deep Learning. Preprint available on arXiv: https://arxiv.org/abs/2006.13807 | ||||||||||
| Blood Cell Subtypes Classification | 7 | 4 years ago | Jupyter Notebook | |||||||
| Using deep learning and CNN model | ||||||||||
| Bbox_gradcam | 6 | 2 years ago | mit | Jupyter Notebook | ||||||
| Boundary box creation using a GradCAM heat-map from a pre-trained image classification model. | ||||||||||
| Cervical Cancer Prediction | 5 | 4 years ago | 1 | gpl-3.0 | Jupyter Notebook | |||||
| In this data set, We have to predict the patients who are most likely to suffer from cervical cancer using Machine Learning algorithms for Classifications, Visualizations and Analysis. | ||||||||||
| Breast Cancer Wisconsin | 4 | 4 years ago | gpl-3.0 | Jupyter Notebook | ||||||
| This is Data set to Classify the Benign and Malignant cells in the given data set using the description about the cells in the form of columnar attributes. There are Visualizations and Analysis for Support. | ||||||||||
| Knn_implementation | 3 | 5 years ago | Jupyter Notebook | |||||||
| K-Nearest Neighbours Algorithm | ||||||||||
| Signatureheatmap | 2 | 17 days ago | R | |||||||
| R package to create heatmaps using signature gene list and transcriptomic data | ||||||||||
| Heatmap_expts | 2 | 4 years ago | Python | |||||||
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, Daniel King and David A. Tuveson
Citation
If you use this package for a publication, we would ask you to cite the following:
Deschnes 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, Deschnes 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
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')
Maintainer
Bugs/Feature requests
Please contact us for bug fixes or with feature requests.
Thanks!
