README.md

In msuefishlab/shinyorthologs: Compare orthologs across species as a RShiny app

shinyorthologs

Shiny interface to an ortholog database

Prerequisites

To get system dependencies, for example on Ubuntu 16, use

sudo apt install r-base-core postgresql libpq-dev postgresql-contrib

Install R dependencies, use devtools

devtools::install_deps()

Load data

The tests/data directory contains an example dataset that can be loaded

If you data is in this format then you can use the create.sql, load_fasta.sh, load_expression.sh, and load.sh scripts, copy these into your own data directory, then run

./load.sh yourdbname

Then copy sample_config.json to config.json and enter the parameters appropriately

Usage

After loading the data, run

shiny::runApp()

or simply put the shinyorthologs application directory in the shiny-server webapps directory.

msuefishlab/shinyorthologs documentation built on May 23, 2019, 8:17 a.m.