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README.md

Degust

  • Visualise RNA-seq differential expression data.
  • Perform your own DGE analysis, or use the inbuilt server to analyse from your own "counts" file.

Access a public web service running Degust

View a short video of the interface in use.

Read a summary on the Degust home page.

Example Screenshots


FAQ

See FAQ.md

How to Cite

DOI

Installation

If you do not want to use the public Degust installation, you may install your own.

You first need to grab a copy of Degust.

    git clone git@github.com:Victorian-Bioinformatics-Consortium/degust.git

Degust can be installed in two ways:

  1. Perform your own DGE analysis, and use only the web frontend from Degust
  2. Install the frontend and back-end software to perform analysis and visualise the results.

Frontend installation only*

!! Frontend installation is only compatible with Python 2.x. Python 3.x will return an error with the module StringIO.

To use the frontend visualisation, you will need to have done your own DGE analysis with a tool like edgeR or voom. You will need CSV file contain a line per gene, and the following columns:

  • ID - containing a unique identifier for each gene (required)
  • Adjusted p-value - The adjusted p-value (FDR or similar) for that gene (required)
  • Log intensity for each condition - Used to compute the log fold-change (required)
  • Average intensity across the conditions - Used for the MA-plot (required)
  • Gene info - Arbitrary information columns to display in the gene list table (optional)
  • Read counts - Read counts for each replicate, only used for display purposes (optional)

The simplest approach is to download degust.py then run it with your csv file as a parameter. This will create a single HTML page that you view or share. Run python degust.py --help to find the parameters to specify the column names for your CSV.

python degust.py --help
Required Arguments: Description
csvfile CSV file to process (default stdin)

Optional Arguments: Description
-h, --help show this help message and exit
-o OUT, --out OUT Output file (default stdout)
--name NAME Name for this DGE comparison
--notour NOTOUR Do not show the tour on first load
--primary PRIMARY Name for the primary condition that the fold-changes are relative to
--avg AVG Name for average intensity column in CSV file
--fdr FDR Name for "FDR" column in CSV file (default "adj.P.Val")
--logFC LOGFC Comma separated names for "logFC" columns in CSV file
--info INFO Comma separated names for info columns in CSV file
--counts COUNTS Specify 'count' columns - only used for display in the table. Specify the name of the logFC column then a colon followed by comma separate count columns. Use multiple times for multiple conditions. Example: --counts cond1:cond1-rep1,cond1-rep2
--link-col LINK_COL Name for column to use with "--link-url"
--link-url LINK_URL Gene info URL. Used when double-clicking the gene-table. Any "%s" will be replaced with the value from the specified "--link-col"
--tab Specify that the csv file is actually tab delimited
--cuffdiff Input file is from cuffdiff (gene_exp.diff). This will set the columns automatically. Note this is still experimental

optional arguments can be used to identify the name of the column required in your csv file

Sample command

python degust.py degust-1.csv --avg AveExpr --fdr FDR --logFC Keap1KO --info symbol --out index.html

Full installation

See INSTALL.md

License

Degust is released under the GPL v3 (or later) license, see COPYING.txt

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