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What's the best way to spend my money on hardware, if I'd like to run SAIGE-GENE on a plink file with 2k samples and a WES data after QC, preferably using docker? How many cpu cores can be utilised in…
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## Background
We want to explore extracting gene/disease associations from the exome sequencing analyses carried out by Regeneron Genetics Center.
Their work is collected in their recent [publicat…
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The Interaction Learner: Interaction Transformer + Generalized Linear Model (Logistic regression mostly I think) seems to fail to converge on the UKBB data. this need investigation.
TODO:
- [x] …
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Hi there!
I am running LDSR analysis using the package you developed, as well as LDSC. However, I noticed that the results (i.e., intercept and h2 estimate) from bigsnpr and LDSC are not similar ev…
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I have a quick question; I am working in African ancestry for both target dataset and summary statistics.
I noticed that in the ldpred2 paper, the European LD reference is available at https://doi.o…
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I installed using conda baghera-v2.1.11 and received the below error when running baghera on the ldscore_folder and GTF file (step1).
("baghera-tool -h" command work well)
NameError: name 'folder…
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Just a note to myself to look into this message that comes up (but doesn't seem to cause an error).
## Reprex
### Data
Download the file *plt.assoc* from here:
*ftp://ftp.sanger.ac.uk/pub/p…
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Hi Taro,
Thanks for this great toolbox! I have a (kind of silly!) question: is it possible to estimae heart fat (I've seen LV mass estimation elsewhere) from neck-to-knee or other modalities availa…
Ojami updated
2 years ago
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Hi Omer,
very nice package, and very easy to use.
However, I found a problem when constructing the LD matrix from a BED file (I use a subsample of UKB).
SuSie runs fine using the wrapper function, …
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also GM volume outputs are in different order than matrix / parcellation look-up table
relevant code here: https://github.com/McIntosh-Lab-RRI/tvb-ukbb/blob/3cebec9f0d26ddfb75b82ea7b5ae678a770eb505…