Using Flexynesis on usegalaxy.eu

Here you will learn how to use the Galaxy platform to utilize flexynesis in multi-omic data integration for clinical variable prediction.

First time using Galaxy?

You can check "Galaxy Basics for everyone" training to learn more about data analysis using Galaxy!

Import a curated dataset

In this tutorial we will use a multi-omic dataset of Lower Grade Glioma (LGG) and Glioblastoma Multiforme (GBM) Merged Cohorts. The data were downloaded from Cbioportal. The dataset was split into 70/30 train/test splits and used as input to Flexynesis.

https://zenodo.org/records/13881580/files/test_clin.csv
https://zenodo.org/records/13881580/files/test_cna.csv
https://zenodo.org/records/13881580/files/test_mut.csv
https://zenodo.org/records/13881580/files/train_clin.csv
https://zenodo.org/records/13881580/files/train_cna.csv
https://zenodo.org/records/13881580/files/train_mut.csv
  • Copy the above link locations.
  • Click Upload at the top of the tool panel.
  • Select Paste/Fetch data.
  • Paste the links into the text field.
  • Press Start.
  • Close the window

Data Upload

The example dataset contains 556 training samples and 238 testing samples. Each sample has both copy number variation and mutation data. The mutation data was converted into a binary matrix of genes-vs-samples where the value of a gene for a given sample is set to 1 if the gene is mutated in that sample, or it is set to 0 if no mutation was found for that gene.

Check the data

Once your data turns green it means it is successfully uploaded to your history. Click on the data and make sure the data format is "CSV".

In case that the format is not CSV (E.g. TXT), you should change it to csv.

  • Click on the pencil icon for the dataset to edit its attributes.
  • In the central panel, click on the Datatypes tab on the top.
  • Click the New Type button and choose csv then click on Save.

Supervised training

Survival

For survival analysis, two separate variables are required: * Survival event: a numeric event variable (consisting of 0's or 1's, where 1 means an event such as disease progression or death has occurred). * Survival time: a numeric time variable, which indicates how much time it took since last patient follow-up.

Let's start the analysis!

Search for "flexynesis" on search tools panel and select the tool.

First you should certify that you are using flexynesis for Research/Educational purposes.

Now continue with the following parameters to do a survival analysis using flexynesis on Galaxy.

  • Type of Analysis: Supervised training

  • Training clinical data: train_clin.csv

  • Test clinical data: test_clin.csv
  • Training omics data: train_mut.csv
  • Test omics data: test_mut.csv

What type of assay is your input? is an optional parameter you can use to name your assay (E.g. cnv here). If not specified it will be named "main"

First Assay

Click on Insert Multiple omics layer? to add the next layer.

  • Training omics data: train_cna.csv
  • Test omics data: test_cna.csv

What type of assay is your input? is an optional parameter you can use to name your assay (E.g. gex here). If not specified it will be named "omics_0"

  • Model class: DirectPred
  • Survival event: OS_STATUS
  • Survival time: OS_MONTHS

Second Assay

Click on Run Tool to start your analysis!

Once the result turns green, the analysis is finished. Click on the dataset to explore the results!

Finished