On this page you will find some information to help you get started with ImmuneSpace. You first task will be to identify data you would like to explore, and this can easily be done using the built-in Data Finder. If you are interested in a single study and you already know the accession number of that study, you can quickly navigate to it via the menu bar, e.g. "Studies > SDY269". Note that since ImmuneSpace data are transferred directly from ImmPort, ImmuneSpace use the same accession number for consistency. So if you have worked with ImmPort data in the past, you might be able to find these data in ImmuneSpace too (not all ImmPort data are transferred to ImmuneSpace).
We have created a few video tutorials (see below) to explore some of the key features of ImmuneSpace.
Did you know that ImmuneSpace has a YouTube channel? This is the best place to get up and running as quickly as possible. You will find videos on:
Overall introduction to ImmuneSpace
This is the first tutorial that will introduce you to ImmuneSpace and show you how to register and login to the site. You will also learn about the main site navigation, how to reach important pages including the support page, and how to access the tutorials.
Exploring a study in ImmuneSpace
This tutorial will show you how to explore a specific study and its associated data in ImmuneSpace. For example, you will be able to learn about the study PI, endpoint, objectives, and other important study data. You will also learn how to browse participant data including clinical and assay data using the built in grid (see tutorial 4 below). Finally, the tutorial will show you how to retrieve the list of reports and analyses available for a given study. You will have the opportunity to learn more about some of these analyses by watching the tutorials 5-8 listed below.
Identifying data of interest using the Data Finder
This tutorial will show you how to use the Data Finder to combine (and possibly filter) data from multiple studies. The resulting data can then be visualized and analyzed using the built-in tools or downloaded for use within your favorite tool.
Working with tabular data in ImmuneSpace
This tutorial will show you how to work and interact with tabular data in ImmuneSpace using the built-in grid. You will learn how to view, filter, sort and export tabular data.
Visualizing immunological data using the Data Explorer
This tutorial will introduce you to the Data Explorer, a new visualization tool that we have built for ImmuneSpace. The Data Explorer can be used to quickly plot a selected immunological response variable (e.g. HAI) in one or more cohorts across multiple analytes (when applicable). Visualization is achieved using the ggplot2 R package, and several graphical options are made available including lines, boxplots and heatmaps. Demographics variables such as gender and age can be added to the plot using aesthetic variables such as color, shape etc.
Correlating gene expression and immunological data
This tutorial will show you how to use the Gene Expression Explorer (GEE) to correlate gene expression data with HAI. The GEE can be used to quickly plot the expression level of one or more genes against a selected immunological response variable (currently HAI, more options coming later) in one or more cohorts. As with the Data Explorer visualization is achieved using the ggplot2 R package. Demographics variables can also be added to the plot using aesthetic variables.
Performing a gene set enrichment analysis in ImmuneSpace
This tutorial will show you how to perform Gene Set Enrichment Analysis (GSEA) in ImmuneSpace. You will learn how to perform GSEA across time within a specified cohort using the CAMERA method of the Limma R package.
We expect to create more videos as the ImmuneSpace community is growing. Feel free to use the support page if you have any comments or suggestions regarding our tutorials.
Finally, since ImmuneSpace is powered by LabKey Server, you might also want to have a look at the existing LabKey tutorials.