Microscope

• Extention and reimplementation of ID-TaXER
• The RShiny app which relies on this code is here
• The code to produce the RShiny app is located in microscope/vignette/app.R
• The main code is in microscope/R/analysis.R which is used to manipulate the data which goes into the RShiny app

Description

Microscope is a package containing a collection of functions which are run as part of the modular workflow to create the RShiny App Microscope.

These functions enable the transformation and combining of spatial data with genomics data.

Installing

The easiest way to install microscope is from GitHub using devtools.

In R run the following commands:

# Install devtools to be able to install packages from GitHub
install.packages("devtools")

# Load devtools and install microscope
library(devtools)
devtools::install_github("NERC-CEH/microscope")

Running

The functions are designed to read in and write out csv files. The documentation should make it clear as to what the structure of the csv files should be. Some functions require additional files, and this is explained in the documentation.

Running the workflow

The workflow which uses microscope can be found here (create repo for notebook) along with documentation on how to run the workflow.

Authors

Authors: Briony Jones

Contributors: Robin Long

Funding Statement

This projected is part of the Environmental Data Service (NERC EDS) pilot, funded under the UKRI Research Cloud Pilot Initiative, Digital Research Infrastructure programme.