Oncobox collections of libraries
Project description
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
-
Create any directory that will be used as a sandbox. Let's assume it is named
sandbox
. -
Extract
resources/databases.zip
intosandbox/databases/
.
(You may download the archive fromhttps://gitlab.com/oncobox/oncoboxlib/-/blob/master/resources/databases.zip
) -
Extract example data
resources/cyramza_normalized_counts.txt.zip
intosandbox
.
(You may download the archive fromhttps://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
- Change directory to
sandbox
and execute the command:
oncoboxlib_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.
Help
usage: calculate_scores.py [-h] --samples-file SAMPLES_FILE
[--controls-file CONTROLS_FILE] [--ttest]
[--fdr-bh] --databases-dir DATABASES_DIR
[--databases-names DATABASES_NAMES]
[--results-file RESULTS_FILE]
Command line tool for calculation of pathway activation level according to
doi: 10.3389/fgene.2021.617059
optional arguments:
-h, --help show this help message and exit
--samples-file SAMPLES_FILE
Table that contains gene expression for cases (or
cases and controls). 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.
--controls-file CONTROLS_FILE
Optional file that contains controls. If provided,
cases and controls will be increased by one and
normalized by quantile normalization.
--ttest Include to result a column for unequal variance t-test
two-tailed p-values (aka Welch's t-test). It is
assumed that cases and norms are independent. t-test
will be performed between all cases and all controls.
--fdr-bh Include to result a column for p-values corrected for
FDR using Benjamini/Hochberg method
--databases-dir DATABASES_DIR
Directory that contains pathway databases. Databases
can be downloaded from https://gitlab.com/oncobox/onco
boxlib/-/blob/master/resources/databases.zip (Biocarta
1.123, KEGG Adjusted 1.123, Metabolism 1.123, NCI
1.123, Qiagen 1.123, Reactome 1.123)
--databases-names DATABASES_NAMES
Names of databases that are used to calculate PALs.
"all" means that all database from --databases-dir
will be used.
--results-file RESULTS_FILE
Output file that will contain results, "pal.csv" by
default
Project details
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