In laurabiggins/spex: spex data exploration

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

spex

The goal of spex is to provide an online tool for simple exploration of biological datasets.

It is currently running here on the Babraham shiny server with an example dataset.

The initial page currently looks like this:

The tabs allow the user to explore a dataset, metadata information and an example plot are shown below.

plot(start_page_screenshot)

Preparing data

Main data file

A data file where each row contains a different genes (or other markers), and each column contains a different sample e.g.

Metadata file

sample names in the first column that must match the column names in the main dataset, then conditions in subsequent columns e.g.

| sample_name | class | time_series | |-------------|--------|-------------| | DAO06 | DA | 1440 | | DAO09 | DA | 1440 | | OEA098 | OEA | 240 | | OEA068 | OEA | 960 | | OEA101 | OEA | 960 |

Keep the name of the first column as "sample_name" - it's simpler for processing.

Installation

This is currently under initial development and has not been released.

# You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. You could also use GitHub Actions to re-render `README.Rmd` every time you push. An example workflow can be found here: <https://github.com/r-lib/actions/tree/master/examples>.

laurabiggins/spex documentation built on Dec. 27, 2021, 8:14 p.m.