Simple statistical and visualisation tool for neuroimaging genetics studies
Project description
NIMAGEN: Statistical and Visualisation tool for NeuroIMAging GENetics studies
See the online documentation for detailed walkthrough of some of the package tools.
Quick install
pip install lehai-ml/nimagen
conda install -c lehai-ml nimagen
Main functions of nimagen
is to
- Perform mass linear regression tests and subsequent stability tests.
- Visualise significant results and plot them on brain maps
- 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.
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