Imaging-transcriptomics
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alegiac95
A package, and script, to perform imaging transcriptomics on a neuroimaging scan.
Dear alegiac95,  Thank you for your toolbox "Imaging-transcriptomics". I have met bug performing this code `(transcriptomics) PS C:\Users\lena> imagingtranscriptomics --input F:/banana/Reslice_7_1.nii --regions cort --no-gsea pls --ncomp 1` The error...
Dear alegiac95, Thanks for providing this great scripts! I am using this toolbox in my project but meeting a bug. After PLS analysis, I obtained .pkl file. When I did...
https://github.com/alegiac95/Imaging-transcriptomics/blob/7ccc56d6bf8c14e4d321c1fc99cfb3fc41cb7be8/imaging_transcriptomics/transcriptomics.py#L166
A more detailed explanation on PLS model and regression is required in the docs. - [ ] Add a general mathematical formulation of PLS - [ ] Use of PLS...
If the --verbose or --suppress are used these don't change the behavior of the script.
In `pls.py`, lines 148-151:  I am confused about why it is `orig.` for genes and z-score, but `boot.` for the p-value and adjusted p-value. As in `genes.py`, within the...
https://github.com/alegiac95/Imaging-transcriptomics/blob/46adb1df85c37123c77226d023b6d763edae8aca/imaging_transcriptomics/genes.py#L116C1-L125C36 Hi, I am wondering if there is some thing wrong with the correlation here. ``` def correlate(c1, c2): """Return the MATLAB style correlation between two vectors.""" return np.corrcoef(np.hstack((c1, c2)),...
Hello, when running 'imt_gsea', I encountered an error: 'TypeError: gsea() got an unexpected keyword argument 'perm_index'.' I've tried various methods but still can't resolve it. Can you help me? The...
Bumps [numpy](https://github.com/numpy/numpy) from 1.21.1 to 1.22.0. Release notes Sourced from numpy's releases. v1.22.0 NumPy 1.22.0 Release Notes NumPy 1.22.0 is a big release featuring the work of 153 contributors spread...
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