oncoboxlib 1.2.1

Oncobox collections of libraries

oncoboxlib

Oncobox library calculates Pathways Activation Levels (PAL) according to Sorokin et al.(doi: 10.3389/fgene.2021.617059). It takes a file that contains gene symbols in HGNC format (see genenames.org), their expression levels for one or more samples (cases and/or controls) and calculates PAL values for each pathway in each sample.

Installation

pip install oncoboxlib

How to run the example

1. Create any directory that will be used as a sandbox. Let's assume it is named sandbox.

2. Extract resources/databases.zip into sandbox/databases/.
   (You may download the archive from https://gitlab.com/oncobox/oncoboxlib/-/blob/master/resources/databases.zip)

3. Extract example data resources/cyramza_normalized_counts.txt.zip into sandbox.
   (You may download the archive from https://gitlab.com/oncobox/oncoboxlib/-/blob/master/resources/cyramza_normalized_counts.txt.zip)

What it looks like now:

   - sandbox
       - databases
           - Balanced 1.123
           - KEGG Adjusted 1.123
           ...
       - cyramza_normalized_counts.txt  

4. Change directory to sandbox and execute the command:

calculate_scores --databases-dir=databases/ --samples-file=cyramza_normalized_counts.txt

It will create a result file sandbox\pal.csv.

Alternatively, you can use it as a library in your source code. For details please see examples directory.

Input file format

Table that contains gene expression. Allowed separators: comma, semicolon, tab, space. Compressed (zipped) files are supported as well.

• First column - gene symbol in HGNC format, see genenames.org.
• Others columns - gene expression data for cases or controls.
• Names of case columns should contain "Case", "Tumour", or "Tumor", case insensitive.
• Names of control columns should contain "Control" or "Norm", case insensitive.

It is supposed that data is already normalized by DESeq2, quantile normalization or other methods.