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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 (…
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Hi Jean,
I am looking to plot the genotype versus the splicing ratio. The sQTLseekeR output has only one relative abundance per gene. Is there a way to output the relative abundance for all the tra…
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Hello Yang @goldenflaw !
I hope I am not bothering you too much.
In `leafcutter_cluster_regtools.py` -> `refine_cluster()`, the junction filtering if-statement is: `if (count / float(totN) >= …
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Hello I found an error when i run the following code in R, Can you help to track this? any suggestion? Thanks.
res.df = sqtl.seeker(tre.df, genotype.indexed.f, gene.bed, svQTL=TRUE)
G118
Sub…
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Question 1
In my case of using rMATs. Too many MXE events in >80% samples (see attached). I also found most differentially expressed splicing events were MXE. Did these reasonable?
[AS_sample_number…
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Similar to the work on variant index (#3350), we would like to serve a `gwas_study_index` dataset through OS + API.
This dataset is created by different upstream ETL processes ([gentropy](https://g…
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## Background
Raised from discussion on slack genetics channel with @Juanmaria-rr.
https://platform.opentargets.org/target/ENSG00000105397/associations
https://genetics.opentargets.org/variant…
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Hi Authors,
I am trying to reproduce the results of Fig3, I was able to run and finish almost all steps except
```
utils_GWAS.plot_enrichment_per_gene_linked_tiles_peaks([pbmc_ukbb_file], ukbb_f…
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I've found it convenient when using cTWAS with sQTL models across multiple tissues (~20k models per tissue) to customize cTWAS to allow for by chromosome `ctwas_rss` parameter estimation/fine-mapping …