GenePiper

GenePiper is a stand alone R shiny application for NGS data mining. It provides over 20 different analysis methods with user-friendly GUI. Recently, 6 main categories (Diversity, Descriptive, Oridination, Correlation, Clustering and Non-parametric) was included.

Installation

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Software requirements:

• VirtualBox

• Vagrant

Installation:

1. Download the Vagrantfile from the above.

2. Create a working directory and copy the Vagrantfile to it.

3. If Vagrantfile contains any extension, e.g. .txt, remove it.

4. Run vagrant up in the working directory.

5. After installation, using any web browser to host machine http://localhost:4002.

Sample data:

Random generated sample data is provided in sampleData folder which contains 4 files. otuTableSample.tsv is a tab separated OTU table file with 100 samples and 2000 taxa. taxTableSample.tsv is a tab separated Taxonomy table file with 2000 taxa and 7 taxonomical rank. samDataSample.tsv is a tab separated sample mapping file with 100 samples and 12 feature columns. treeSample.tre is a phylogenetic tree file with 2000 taxa.