Readme

Logging In

The default username and password for QuaCRS is:
Username: user
Password: password

Installation Readme

Latest Installation Readme (Updated 7/11/14)

Site Manual

Sample View

This is the home view for the QuaCRS database. It is accessible from any other page by clicking the QuaCRS logo at the top left of the page.

There are four main aspects to the Sample View page:
  1. The Search Bar – used to search for specific samples. To use, type a query and select Search. To only search a specific column, enter "Column:Term" (ex: "Study:Study1").
  2. The Select Columns Menu – A dropdown menu used to change which information is visible in the Sample View. Information is organized into descriptive subcatagories. Clicking on any category will open or close it to allow columns to be selected. Checking or unchecking a box shows or hides that information for all samples. Note that some samples may not have data for certain columns, in which case that column will be blank for that sample.
  3. The Aggregate button. This button is used to generate Aggregate Results for multiple samples (described below).
  4. The Sample List – Each row in this list is a different sample. The visible columns can be selected by the Select Columns Menu. The checkboxes to the left of each sample are used to select samples for use in Aggregate Reports. Clicking on a sample name will display Sample Details for that sample (described below). Clicking on the header of a column sorts the samples by that column and columns can be reordered via drag and drop.

Sample Details

This page shows a detailed overview of the QC for a specific sample. QC is organized into descriptive subcatagories. Clicking the Download Report button will download an Individual Report (described below). Clicking the Show/Hide button will show or hide a specific section, allowing other sections to be viewed more easily. The Duplicate Stats and Plots sections can also be shown or hidden by clicking on the label. Clicking on a plot will zoom in on it. In this view, the arrow keys can be used to scroll between plots.

Individual Report

An Individual Report is a CSV table containing two lines – a header line, and a data line. It contains all of the same QC information as the Sample Details page. Images are not included, but are listed as filename paths from the root data directory.

Aggregate Results

The Aggregate Results page is similar to the Sample Details page, except it can describe multiple samples. Most values are outlined as minimum, average and maximum values across the selected samples. The qualitative FastQC values are outlined by the count of samples that passed, failed or received a warning. Clicking the Show/Hide Details button above the FastQC Stats section will provide more or less information on the FastQC results. Clicking the Download Report button will download an Aggregate Report (described below). Unlike the Sample Details page, the Aggregate Results page does not include plots, since the number of plots quickly becomes impractical when viewing many samples.

Aggregate Report

An Aggregate Report is identical to an Individual Report, except that it can contain more than two lines. The first line is still the header, and every line after it is a different sample.

Other Pages

There are several other pages in the QuaCRS interface which are accessible by clicking the links at the top of any page:
  1. The Downloads page contains links to download QuaCRS, as well as a version history.
  2. The About Us page contains information about The Ohio State University Comprehensive Cancer Center, as well as contact information for the maintainers of this site.
  3. The Readme page contains this manual as well as a link to the latest Installation Readme for QuaCRS.