NIMAGEN: Statistical and Visualisation tool for NeuroIMAging GENetics studies

See the online documentation for detailed walkthrough of some of the package tools.

Quick install

1. pip install lehai-ml/nimagen
2. conda install -c lehai-ml nimagen

Main functions of nimagen is to

1. Perform mass linear regression tests and subsequent stability tests.
2. Visualise significant results and plot them on brain maps
3. Visualse gene-set based analyses results

Cite

If using this package, please cite the following paper

Le H, Dimitrakopoulou K, Patel H, Curtis C, Cordero-Grande L, Edwards AD, Hajnal J, Tournier JD, Deprez M, Cullen H. Effect of schizophrenia common variants on infant brain volumes: cross-sectional study in 207 term neonates in developing Human Connectome Project. Transl Psychiatry. 2023 Apr 10;13(1):121. doi: 10.1038/s41398-023-02413-6. PMID: 37037832; PMCID: PMC10085987.

Example of a plot created with nimagen

Figure 1. Example map of brain regions with accompanying legend

Figure 2. Example regression multiple-plot

Version update

• 0.0.2 - 20 March 2023 - Revamped stats module to use patsy format instead.
• 0.0.1 - First version

Things to improve

• genes.py - fix the bed_reader.to_bed, currently, the val and properties dict do not match up.
• genes.py - update the calculate snp associations, so that it can take in categorical data without dummy variables.