User: Robert Castelo

gravatar for Robert Castelo
Robert Castelo2.1k
Reputation:
2,080
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Trusted
Location:
Spain/Barcelona/Universitat Pompeu Fabra
Website:
http://functionalgenom...
Twitter:
robertclab
Scholar ID:
Google Scholar Page
Last seen:
2 weeks ago
Joined:
10 years, 6 months ago
Email:
r*************@upf.edu

Associate professor of Bioinformatics and Biostatistics at the Universitat Pompeu Fabra in Barcelona (Spain). PhD in Computer Science by the University of Utrecht, The Netherlands (2002).

I develop and maintain the R/BioC software packages qpgraph, GenomicScores and VariantFiltering and have contributed to the development of the GSVA and tweeDEseq software packages. I'm also contributing and maintaining the annotation packages phastCons100way.*, MafDb.* and fitCons.UCSC.hg19, and some AnnotationHub resources available from the GenomicScores package.

Posts by Robert Castelo

<prev • 260 results • page 1 of 26 • next >
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Answer: A: Error thrown by GSEABase::getBroadSets function: Error: 'getBroadSets' failed to
... hi, I've just tried it out with the current release version of R 3.4.2 and the GSEABase package (1.40.1) and it works fine. You need to update to the  current R release version 3.4.2 and current release of Bioconductor; see http://bioconductor.org/install. library(GSEABase) MSigDB <- getBroadS ...
written 4 weeks ago by Robert Castelo2.1k
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Comment: C: [gwascat] Updated GWAS catalog from file
... I see three options: write a wrapper function for your students, parse the gwascat file yourself and provide your students directly with the 'GRanges' object, or contact the package maintainer to request further functionality. ...
written 5 weeks ago by Robert Castelo2.1k
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Answer: A: [gwascat] Updated GWAS catalog from file
... Assuming the downloaded file is called 'gwas_catalog_v1.0.1-associations_e90_r2017-09-12.tsv', what about gwascat <- read.delim("gwas_catalog_v1.0.1-associations_e90_r2017-09-12.tsv", sep="\t", header=TRUE, stringsAsFactors=FALSE) ? just look at the source code of 'makeCurrentGwascat()' and y ...
written 5 weeks ago by Robert Castelo2.1k
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Answer: A: Gene missing in TxDb.Hsapiens.UCSC.hg19.knownGene
... hi, indeed, if you try to access the annotation of the gene with the 'genes()' method and its default parameters, you won't find it: "8831" %in% names(genes(txdb)) [1] FALSE however, the gene forms part of this annotation package and you can see it if you use the 'exonsBy()' method: library(T ...
written 7 weeks ago by Robert Castelo2.1k
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Comment: C: How to set 'strandMode' with summarizeOverlaps()
... Thanks for the directions and your sample code. Unfortunately, I can't use it because it assumes that the whole thing fits into main memory. I'll paste my solution for the record, just in case becomes useful for somebody else interested in using the non-default 'strandMode=2': ## settings with res ...
written 9 weeks ago by Robert Castelo2.1k
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Comment: C: How to set 'strandMode' with summarizeOverlaps()
... I guess you refer to 'singleEnd' when you say 'pairedEnd', but anyway, now I understand that if I want to set 'strandMode' I need to set 'fragments=FALSE' to force the call to 'readGAlignmentPairs()'. Unfortunately, that does not work either: se <- summarizeOverlaps(genefeatures, bfl, mode="Uni ...
written 9 weeks ago by Robert Castelo2.1k
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Comment: C: How to set 'strandMode' with summarizeOverlaps()
... Hi Jim, I had already tried setting that argument through summarizeOverlaps(), BamFileList() and ScanBamParam() and I get an error. Here's an example reproducing the error: library(GenomicAlignments) library(pasillaBamSubset) library(TxDb.Dmelanogaster.UCSC.dm3.ensGene) txdb <- TxDb.Dmelanogas ...
written 9 weeks ago by Robert Castelo2.1k
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How to set 'strandMode' with summarizeOverlaps()
... Hi, I want to build a table of counts using 'summarizeOverlaps()' from a PE RNA-seq data set generated with a strand-specific library preparation protocol from NewEngland Biolabs called "NEBNext Ultra Directional RNA Library Prep Kit for Illumina". The web page from that protocol says that it "util ...
genomicalignments written 9 weeks ago by Robert Castelo2.1k
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Comment: C: How to build a RNA-seq table of counts for repeatmasker annotations
... True, that was it, thanks! ...
written 10 weeks ago by Robert Castelo2.1k
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Comment: C: How to build a RNA-seq table of counts for repeatmasker annotations
... thanks for the tip. i've seen that section 5.1 of the vignette of rtracklayer contains an example about importing repeatmasker annotations for genomic regions. however, because i need to work with the whole set of annotations, i can't use that approach since it would take too long. i've downloaded t ...
written 11 weeks ago by Robert Castelo2.1k

Latest awards to Robert Castelo

Scholar 7 months ago, created an answer that has been accepted. For A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
Supporter 8 months ago, voted at least 25 times.
Scholar 8 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 8 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 11 months ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Scholar 11 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 21 months ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 2.1 years ago, created an answer that has been accepted. For A: Network generation from adjacency matrix of zeroes and ones
Scholar 2.2 years ago, created an answer that has been accepted. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 2.2 years ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 2.7 years ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 2.7 years ago, created an answer that has been accepted. For A: phastCons scores for GRCh38
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Autobiographer 3.3 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.5 years ago, created 100 posts.

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