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Hi Min Cheol,
I want to do an analysis in which cells come from multiple donors and I would like to perform differential gene expression analysis in a non-pseudobulked format. I do not have SNP inf…
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I need the following files to run `scripts/07-format_nephqtl2_coloc.R`:
- `eQTLs_chrAll_40_peers_cis1000kb_Glom.NephQTL2.txt.gz`
- `eQTLs_chrAll_50_peers_cis1000kb_Tube.NephQTL2.txt.gz`
Could y…
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Hi,
I am a new user of the `coloc` package and need clarification on how to correctly set up input parameters, particularly `MAF`, `N`, and `sdY`. I am working with GWAS and eQTL data, where the GW…
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Hello tensorqtl team,
We are using tensorqtl to conduct eQTL analysis in our datasets and while computing permutations for the cis-eQTL to get empirical values we encountered this error.
ten…
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Hello,
I want to check whether I can run qpgraph in parallel, and I find that SnowParam with MPI backend is used in the source code.
I try the sample data generated in vignette and run the qpgr…
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### Contact Details
jianan.luan@mrc-epid.cam.ac.uk
### Scripts
03d-non_genetic_methylation_pcs.sh
### What happened?
the script ./03d-non_genetic_methylation_pcs.sh failed with an error message "…
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Hi,
Thank you very much for sharing such an impressive work. I would like to run MR-JTI analysis but I don't know how to obtain data from eQTL, I mean beta, se and p-value. In addition, I thought t…
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Hello, I'm using mashr for my research, and I'm trying to discriminate eQTLs which are same or different among conditions.
I've seen a tutorial from vignette, which uses `get_pairwise_sharing_from_sa…
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Hi there!
Thank you for the practical package. I have a question regarding the coloc.abf function when running it between my eQTL and GWAS data, both derived from the same samples. Here’s the code …
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Hi,
I am encountering an issue when running the eqtl_prepare_expression.py script. Specifically, I get an AttributeError stating that module 'qtl.io' has no attribute 'sort_bed'. I'm running it usi…