User: enricoferrero

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enricoferrero550
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United Kingdom
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Posts by enricoferrero

<prev • 116 results • page 1 of 12 • next >
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Comment: C: keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... Yep, this solves it, thank you. Feel free to add it as an answer so I can accept it. ...
written 4 months ago by enricoferrero550
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Comment: C: keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... This is cool but, is there a way to grab the EnsDb object without having to look up its name in the AnnotationHub (i.e.:  AH53211)? BTW, I didn't mean to hijack my own thread : i still get that error when trying to access the EnsDb objects with keys() or genes(). ...
written 4 months ago by enricoferrero550
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Comment: C: keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... Also, I get the same error when using genes(EnsDb.Hsapiens.v75, columns = "gene_id")$gene_id ...
written 4 months ago by enricoferrero550
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Comment: C: keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... Hi Johannes, thanks for the quick reply. I updated the post with the sessionInfo() output. Does that mean that the standalone packages are no longer maintained? What's the recommended way to load an EnsDb object for a particular version of Ensembl? Thanks! ...
written 4 months ago by enricoferrero550
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keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... Since upgrading to Bioconductor 3.5 I get this error when running AnnotationDbi::keys() on EnsDb.Hsapiens.v75 or other ensembldb objects: > library(EnsDb.Hsapiens.v75) Loading required package: ensembldb Loading required package: BiocGenerics Loading required package: parallel Attaching packag ...
ensembldb ensdb.hsapiens.v75 keys written 4 months ago by enricoferrero550 • updated 4 months ago by Johannes Rainer950
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Comment: C: What is the confidence interval in ChIPseeker::plotAvgProf?
... What is it that is being estimated? And what is it that is being resampled? ...
written 5 months ago by enricoferrero550
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What is the confidence interval in ChIPseeker::plotAvgProf?
... I'm using the plotAvgProf() function from the ChIPseeker package. Can someone explain what does the confidence interval that can be drawn around the peak represent, exactly? See section 4.2.2 of the ChIPseeker vignette for reference. Thank you! ...
chipseeker written 5 months ago by enricoferrero550
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Assign custom dendrogram to ComplexHeatmap Heatmap object
... Hello, Is there a way to assign a custom (row) dendrogram and ordering to a Heatmap object generated by ComplexHeatmap Heatmap() function? After finding out about the row_dend() and row_order() functions, I would have thought something like this would work: library(ComplexHeatmap) mat <- mat ...
dendrogram heatmap heatmap.2 complexheatmap dendextend written 10 months ago by enricoferrero550 • updated 10 months ago by jokergoo90
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Enrichment of GWAS SNPs in regulatory regions
... Hello, I'm trying to perform an analysis similar to those in ENCODE or FANTOM publications where enrichment of GWAS SNPs in regulatory regions (e.g.: DHSs, CAGE-defined enhancers) is calculated [1,2]. So, I would like to calculate if a set of GWAS SNPs associated with a disease of interest is enri ...
genomicranges enrichment fisher written 11 months ago by enricoferrero550
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Comment: C: Clarifications on p-values in enrichResult objects
... Thanks! Are pvalueCutoff and qvalueCutoff combined with an AND or an OR? In other words, do both or either conditions need to be satisfied? ...
written 12 months ago by enricoferrero550

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Student 5 months ago, asked a question with at least 3 up-votes. For Can't upgrade to Bioconductor 3.3?
Popular Question 5 months ago, created a question with more than 1,000 views. For biomaRt proxy issues
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Scholar 17 months ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
Popular Question 17 months ago, created a question with more than 1,000 views. For Linkage disequilibrium with 1000 Genomes/HapMap
Popular Question 17 months ago, created a question with more than 1,000 views. For How to properly sort GRanges?
Popular Question 17 months ago, created a question with more than 1,000 views. For Simple pathway enrichment analysis for gene lists
Popular Question 17 months ago, created a question with more than 1,000 views. For [DESeq2] Cook's distance flagging for continuous variables
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Scholar 17 months ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
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