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Hi
I noticed you chose to normalize intron usage of one sample by RINT cross all intron rather than normalize one intron cross all samples as GTEx eQTL did, I really don’t understand the reason for…
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Hi, thanks for developing and maintaining such an excellent tool.
I am trying to use TensorQTL to analyze some methylation data. I'm thinking of taking a similar strategy as eQTL and sQTL, where a …
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Dear author:
I am really sorry to disturb you. When using fastqtl_to_mashr.ipynb to detect cell-type-specific sQTL coming from AIDA datasets(nominal pass), we come across the following two main pr…
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Hi
I am trying to do a fine-mapping for my eQTL and sQTL data, followed by colocalization with GWAS. I am wondering how to make my grid file. I only have one study so I know that I can set phi to z…
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In Stingray, we build documentation from a bunch of rst files and a number of notebooks. It usually works quite well, but today I'm having errors like the ones in the build below:
https://github.co…
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Hi ! where can I find gtex.db ?
thanks
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Dear Developers,
I wanted to reach out regarding an issue I encountered while running the sqtlseekR2 analysis on the Biowulf server at NIH.
While using a distance bin of +1 Mb from the gene body…
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*Briefly* looking through the code here, it seems like the basic algorithm (correlation + bootstrapping) is extendable to more than two conditions. This would in effect turn your DE software into a po…
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Hello!
I used fastQTL to conduct an sQTL identification, the command is as follows:
fastQTL.static --vcf merged.vcf.gz --bed Osa_perind.counts.gz.qqnorm_Chr1.gz --cov Osa_perind.counts.gz.PCs.PC5 --…
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- [ ] Finish molQTL plotting scripts and plot coverage data for bunch of Colocalized QTL effects
- [ ] Add more GWAS. Need to edit some scripts to accommodate binary outcomes for some gwas... see (…