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Overview
In CZ ID, samples are organized by projects and type of pipeline. Here we describe the Discovery page, which is your "home base" for operating within CZ ID and the default page you will see when you log in to your account.
Discovery Page Layout
When you first log in to your CZ ID you will see what we refer to as the Discovery page under "My Data". This page lists all the projects, samples, and visualizations within your account under tabs for each of these categories. Numbers by each of the tabs indicate the total number of projects, samples, and visualizations (i.e., created heatmaps and phylogenetic trees) in your account. You can sort, filter, and search data within Projects and Samples tabs to quickly find samples of interest.
Projects Tab
By default, you will see the Projects tab within the Discovery page when you log in. This page contains a table summarizing project information and privacy status. You can sort the table based on the header of choice. Click here to learn how to sort the table. To view samples and data associated with a project of interest in the Project page, simply click on a project listed within the Project Table.
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Privacy Status Icons: Use icons to keep track of public (
) and private (
) projects within your account.
- Project Table: Summarizes general information about projects in your account, including:
-
-
- Project name
- Date the project was created
- Hosts for samples included within a project
- Sample types included within a project
- Counts for samples that ran through different pipelines within a project. Pipelines include metagenomic (mNGS) analysis, antimicrobial resistance (AMR) gene detection, and viral consensus genome (CG) generation.
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The Projects tab also includes Filter and Project Information panels. Use the Filter panel on the left side of the page to find projects based on taxon information and metadata. Click here to learn more about filtering data. The Project Information panel on the right-hand side of the page provides general information and statistics for all the projects found in your account. This information will enable you to quickly visualize the distribution of projects in your account based on metadata.
- Filter Icon: Summarizes number of applied filters. Click the icon to show or hide the filter panel.
- Filter Panel: Provides options to filter projects based on specific taxa and/or metadata.
- Information Icon: Click the icon to show or hide the Information panel.
- Information Panel: Summarizes sample distribution based on metadata.
Samples Tab
All the samples in your account will be listed under the Samples tab within the Discovery page. The view under the Samples tab includes Filter and Information panels also available through the Projects tab. You can use the filter options to quickly find samples of interest. Use the sample information panel on the right-hand side of the page to quickly visualize the distribution of samples in your account.
- Pipeline Tabs: Use tabs to navigate samples by pipeline. Numbers by each tab represent the total number of samples ran through each pipeline.
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Toggle: Use toggle to see a list of samples within a sample table (
) or a map showing sample distribution (
) . Only available for samples under the Metagenomics tab (Illumina pipeline).
- Sample Table: Summarizes sample information and privacy status.
- Add Dropdown Menu: Use this menu to customize the table view by adding or removing columns.
Sample information is summarized within the Sample Table. You can sort the table based on the header of choice. Note that metrics and metadata listed in the Sample Table will vary depending on the pipeline. Simply click on a sample of interest to view results.
Visualizations tab
The Visualizations tab within the Discovery page contains all saved visualizations (i.e., created heatmaps and phylogenetic trees) within your account and their privacy status. The Visualization Table summarizes the type of visualization, the date it was created, the project, and the number of samples included in the analysis.
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