User: rodd

gravatar for rodd
rodd130
Reputation:
130
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Trusted
Location:
London, United Kingdom
Twitter:
@3RDuarte
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1 week, 6 days ago
Joined:
5 years, 8 months ago
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r***************@gmail.com

Posts by rodd

<prev • 52 results • page 1 of 6 • next >
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Answer: A: Best practices in eQTL analysis
... I think a good starting point is the GTEx documentation, here: https://www.gtexportal.org/home/documentationPage#staticTextAnalysisMethods They also have published all their scripts (although frankly, I find them a bit complicated, as I switched to bioinformatics in the last 2-3 years or so, so I'm ...
written 8 weeks ago by rodd130
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Comment: C: Surrogate variables in eQTL studies
... Hi Asaf! Sorry I didn't clarify: those would be the first 5 population covariates calculated in plink. ...
written 8 weeks ago by rodd130
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Comment: C: Covariates for eQTL analysis
... I also struggled to install PEER, and ended up opting for `sva`, which is much simpler and well-documented. ...
written 8 weeks ago by rodd130
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Surrogate variables in eQTL studies
... Hi folks! I've got two questions about including surrogate variables in expression analyses. In the GTEx documentation, they say: > "A set of covariates identified using the Probabilistic Estimation of > Expression Residuals (PEER) method (Stegle et al., PLoS Comp. Biol., > 2010 ), calcu ...
sva deseq2 covariates eqtl gtex written 8 weeks ago by rodd130
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Comment: C: RNAseq Normalization for eQTL Mapping?
... Hi Kevin! [Sorry for jumping in on this question... :P ] I would like to perform an eQTL mapping analysis using QTLtools or fastQTL, but I am not sure how I should normalize or transform the count/expression data. [I noticed that if I use just regular DESeq2-normalized values, or variance stabilized ...
written 8 weeks ago by rodd130
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Comment: C: How to get all genes for a specific list of regions in R preferably using Biomar
... After an hour I found out the function that retrieves the names lol.... names_of_genes <- names(gene_list) ...
written 12 weeks ago by rodd130
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Comment: C: How to get all genes for a specific list of regions in R preferably using Biomar
... I think these libraries have changed how they output the genomic ranges objects. > gene_list <- subsetByOverlaps(genes(TxDb.Hsapiens.UCSC.hg19.knownGene), mycoords.gr) > gene_list GRangesList object of length 190: $`100126349` GRanges object with 1 range and 0 metadata ...
written 12 weeks ago by rodd130
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Hi [Kevin Blighe][1], thanks for this incredible tutorial! I was wondering: having obtained the plink.eigenval and plink.eigenvec files using plink's --pca function, is there an objective way of identifying how many population covariates should be included in downstream genetic analyses (e.g. genera ...
written 3 months ago by rodd130
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Answer: A: Testing similarity between functional genomic annotations
... I am calculating the similarity between long binary vectors (80 million in length) in R by importing my annotations as matrices (with each column corresponding to an annotation, and each row corresponding to the base pair position in the genome [0/1 if the SNP belongs to an annotation or not]). I am ...
written 9 months ago by rodd130
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Testing similarity between functional genomic annotations
... Hi folks! I have 1000+ binary vectors of the same length that consist of 0/1 positions corresponding to variants in the human genome and their functional annotation (i.e. transcription factor binding sites, protein-coding regions, methylation sites, etc.). Thus, each vector differs in the order, fr ...
functional genomics garfield genomic annotations R written 10 months ago by rodd130

Latest awards to rodd

Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Best practices in eQTL analysis
Scholar 8 weeks ago, created an answer that has been accepted. For A: Best practices in eQTL analysis
Popular Question 11 weeks ago, created a question with more than 1,000 views. For trimming fastq files with Trimmomatic
Voter 11 months ago, voted more than 100 times.
Student 11 months ago, asked a question with at least 3 up-votes. For Effect of gene size on WGCNA
Supporter 24 months ago, voted at least 25 times.
Epic Question 3.4 years ago, created a question with more than 10,000 views. For trimming fastq files with Trimmomatic
Great Question 3.6 years ago, created a question with more than 5,000 views. For trimming fastq files with Trimmomatic
Popular Question 5.1 years ago, created a question with more than 1,000 views. For trimming fastq files with Trimmomatic

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