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GeneCT: Generalizable Cancerous-status and Tissue-of-origin classifier
based on deep learning appraoch

  GeneCT is free for academic, nonprofit, and personal use under the
  Creative Commons Attribution-NonCommercial 4.0 International License.

However, a license is required for commercial usage. Please contact the author for more inquires.

Download package

Click here to download the latest release of GeneCT (v1.0, Apr 2018; for GNU/Linux x86_64 platform).

The package contains programs, models as well as testing dataset.

GeneCT webserver

Click here to submit your data and run GeneCT on our webserver.

How to run GeneCT

A shell script is provided to run GeneCT on the testing dataset:

    user@linux$ ./run.testing.dataset.sh

Note that the "neuralnet" package for R is required so please make sure you have installed this package before running GeneCT.

Meanwhile, please make sure that your RNA-seq data is processed using TCGA's RNA-seq processing pipeline (i.e., reads were
aligned to the human genome using MapSplice and expression was quantified/normalized using RSEM against UCSC genes).

For more information please refer to README file in the package.

Supplementary datasets

We provide the following preprocessed datasets (as described in the paper) for further testing:
(Detailed information and GeneCT prediction results could be found in Suppl. Table S3)

Citation

When referencing, please cite "Sun K, Wang J, Wang H and Sun H (2018):
GeneCT: a generalizable cancerous status and tissue origin classifier for pan-cancer biopsies.
Bioinformatics 2018, Dec 1; 34(23):4129-4130" PubMed   Full Text

Contact

For more inquiries, please contact the authors.


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