-
I used tensorQTL 1.0.7 to run cis-eQTL, and my BED file wasn’t sorted. However, in version 1.0.8, the BED file must be sorted; otherwise, it gives an error saying, “Positions in BED file must be sorte…
-
Hi there,
I'm interested in using mvsusieR (fit_rss) to fine-map my single-cell eQTLs and estimate the cell-type-specificity of their effects.
I'd like to make sure I did it correctly.
1. estim…
-
Hi Gao,
I am wondering whehter eQTL-twosample-Mendelian Randomization workflow is included in this project.
Thanks.
Shicheng
-
Quick Q. We're using `splatter` to simulate 3 vs. 3 samples from 2 conditions, 3 clusters. However, it seems condition-differences `cde` are introduced "global"ly, i.e., all the same for every `de` gr…
-
This is my command:
!python /Users/halk/MetaXcan/software/SPrediXcan.py \ --model_db_path /Users/halk/Downloads/eqtl/mashr/mashr_Whole_Blood.db \ --covariance /Users/halk/Downloads/eqtl/mashr/mas…
-
Hello MetaXcan
I am trying to use SPrediXcan.py with the mashr Brain_Cortex training model db file, covariance file txt.gz, and GWAS summary data(chromosomes information compiled in just one text fi…
-
Dear developer,
We would like to perform TWAS analysis on a plant population. Our data consists of phenotypes, whole-genome gene expression levels, and genotypes for each sample.
We do not have …
-
Hi developer,
I used your script to calculated the log2afc of my eqtl data. Fortunately, it worked and go…
-
Dear Marc Jan Bonder,
I am following your paper published in Genome Biology (2021) to perform cell-type specific sc-eQTL mapping. In the paper, you mentioned a model including two random effects (k…
-
TensorQTL: https://github.com/broadinstitute/tensorqtl (Check documentation)
Code from MDDseq: https://github.com/LieberInstitute/goesHyde_mdd_rnaseq/tree/master/eqtl/code
[Data conversion](http…