This repository has all the code and tidy data for the analyses in Bertelsen et al.,
The code directory has all of the code for running the primary analyses.
The data directory houses tidy data generated for each step.
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AFNI (https://afni.nimh.nih.gov/) - for preprocessing
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FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) - for preprocessing and ICA
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Python 2.7 from the Anaconda distribution (https://www.anaconda.com/distribution/)
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meica 3.2 (https://bitbucket.org/prantikk/me-ica) - for running ME-ICA preprocessing.
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nibabel (https://nipy.org/nibabel/) - used by
dvars_me.py.
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R 3.5.1 or higher and RStudio (https://rstudio.com/)
- R libraries
c("here","ggplot2","rjson","readxl","reshape2","WGCNA","nlme", "caret","e1071","pheatmap","NbClust","grid","patchwork","psych", "matlabr","circlize","scico","knitr") -
MATLAB R2018b or higher (https://www.mathworks.com/)
- FSLNets (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLNets) - Used for computation of partial correlations to estimate connectivity.
_01_preproc.Rmd - initial processing of NDAR and LEAP ADI-R data (e.g., scoring)
_02_subtyping_final.Rmd - subtyping analyses
_03_connectivity_final.Rmd - connectivity analyses
_04_gex_decoding_final.Rmd - gene expression decoding and enrichment analyses