In ergonyc/omicser: NDCN Omics Browser

knitr::opts_chunk$set(echo = TRUE)

Getting started visualizing data

The browser interface of the application is fairly intuitive. Each of the main sections of the browser are described below, and reference the tabs available for selection near the top of each page.

All aspects of the browser are customizable. This means that there may be differences in what you see compared to the defaults that are described below. Please consult with the person who curated your browser for more information.

Welcome

This page is loaded by default when launching the browser. It includes some basic information about the browser project, as well as a set of instructions in the lefthand side bar.

Ingest

This page allows you to choose the database you will be browsing. Select the database you are visualizing from the drop-down menu (if your app is only visualizing a single dataset, it should appear by default), then click "Load database."

Playground

• identify comparisons to visualize using the "Side Selector" (left browsing bar). e.g.
• choose subsets of data
• specify target features
• choose grouping features
• select type of visualization from tabs:
• Expression - annotated heatmaps
• Diff. Expr. - volcano plots of the differential expression
• Table - a table browser for distribution of expression

Data table

• browse the anotation tables for
• features and
• samples
• browse a "wide" version of the differential expression table

Help

• links to
• the github repo
• this documentaion site

An example browsing session

Under construction

Troubleshooting FAQs

• My visualization isn't loading! The performance of the application is contingent on the amount of data it is processing. If the visualizations you have selected are lagging (or not loading at all), select a smaller subset of data.

ergonyc/omicser documentation built on June 15, 2022, 3:02 p.m.