Questions tagged [gtex]
The gtex tag has no usage guidance.
7
questions
1
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0
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39
views
Applying colocalization analysis in Asian populations
I am planning to add colocalization method as a post-GWAS analysis in my study which is solely based on east Asian populations. I have noticed that coloc, enloc and eCaviar are being commonly used for ...
- 21
1
vote
1
answer
71
views
How to extract column from a matrix matching the another file (sample file)
I have two files master file.txt and sample.txt
master.txt
...
- 395
2
votes
2
answers
670
views
How to remove batch effect from TCGA and GTEx data
I want to play some differentially expressed genes for gliomas cancer. I collected cancer tissue profiles from the TCGA database and normal tissue profiles from the GTEx database. I straightforward ...
- 21
0
votes
1
answer
99
views
Pointing Cromwell to local EBS mounted storage on AWS Batch
I'm trying to run the WDL tasks from the GTEx RNA-Seq pipeline with Cromwell using AWS Batch as a backend.
I store the STAR alignment index on an Elastic Block Store since my Cromwell server instance ...
- 105
1
vote
2
answers
71
views
tabix indexing a GTEx variant file- ':' delimited
I have a gtex variant file- the head of which looks as follows:
...
- 111
1
vote
1
answer
58
views
Is there a single cell RNAseq equivalent of GTEx or TCGA? [closed]
Or do I need to find individual studies and obtain data the long way!
- 11
1
vote
1
answer
193
views
Available phenotype data from GTEx
I am using gene expression data from the The Genotype-Tissue Expression (GTEx) project, available here: http://gtexportal.org. I would also like to use phenotype data for each sample (especially age, ...
- 205