User: Robert Castelo

gravatar for Robert Castelo
Robert Castelo2.4k
Reputation:
2,360
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Trusted
Location:
Spain/Barcelona/Universitat Pompeu Fabra
Website:
http://functionalgenom...
Twitter:
robertclab
Scholar ID:
Google Scholar Page
Last seen:
6 days, 21 hours ago
Joined:
12 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 • 304 results • page 1 of 31 • next >
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Answer: A: generate a phastCons GScores annotation object from 7G hg38.phastCons30way.bw fi
... hi Paul, the way in which annotation packages can be created is not explained and i realize now i should write something about that in the vignette, although we already wrote in the conclusions of the [GenomicScores paper](https://academic.oup.com/bioinformatics/article/34/18/3208/4987140) that "Ad ...
written 6 days ago by Robert Castelo2.4k
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Answer: A: gpr format microarray analysis
... A good starting point is probably one of the available Bioconductor workflows for the analysis of microarray expression data, for instance, [this one](http://bioconductor.org/packages/release/workflows/html/maEndToEnd.html). However, that workflow is about Affymetrix microarray data and you mentione ...
written 8 days ago by Robert Castelo2.4k
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Comment: C: Dealing with duplicated genes in camera gene set testing
... Maybe others in this forum know better about these issues but my impression on the gene id business is that annotation sources, such as [Entrez](https://www.ncbi.nlm.nih.gov/gene) ([Maglott et al., 2011](https://academic.oup.com/nar/article/39/suppl_1/D52/2507756)) or [Ensembl](https://www.ensembl.o ...
written 27 days ago by Robert Castelo2.4k
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Comment: C: Dealing with duplicated genes in camera gene set testing
... For future readers of this post, I'd like to make the argument that on the basis of this answer the original question ``` 1) Is it possible to get the MSigDB gene sets in ensembl format so that I can skip any conversions? ``` can be answered positively, by interpreting "to get the `MSSigDB` gene s ...
written 29 days ago by Robert Castelo2.4k
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Comment: C: mm10 phastCons data for use with ATACseqQC
... hi, to use the release version of Bioconductor you should follow the instructions at [http://bioconductor.org/install](http://bioconductor.org/install), which implies installing a release version of R (3.6.x) and then following the rest of the instructions. to check whether you've successfully ins ...
written 29 days ago by Robert Castelo2.4k
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Comment: C: mm10 phastCons data for use with ATACseqQC
... hi, thanks for reporting this problem. We're transitioning the server that hosts genomic scores available through the AnnotationHub from a http:// protocol to a SSL-compliant https:// protocol and it will take a few days until this transition is complete. in the meantime, we've just autogenerated a ...
written 4 weeks ago by Robert Castelo2.4k
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Answer: A: Dealing with duplicated genes in camera gene set testing
... hi, an alternative is to use the [GSEABase](https://bioconductor.org/packages/GSEABase) sorcery. Let's say you downloaded the GMT file for the MSigDB C2 gene set collection using HGNC gene symbols from: http://software.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/msigdb/7.0 ...
written 4 weeks ago by Robert Castelo2.4k
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Answer: A: How to build and map to a "pre-mRNA" reference transcriptome for single nucleus
... I recently had to deal with intronic reads from a bulk total RNA sequencing experiment (see Fig. 1a from this [preprint](https://www.medrxiv.org/content/10.1101/19000109v2)) and derived an intronic annotation for that purpose using Bioconductor. Our aim was to count strictly intronic reads. If this ...
written 3 months ago by Robert Castelo2.4k
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Comment: C: SVA for repeated measures design
... If `SUBJECT.ID` is a random factor, then you should not put it into the design matrix and use `duplicateCorrelation()` and the arguments `correlation` and `block` in the call to `lmFit()`; see section on Multi-level experiments from the limma User's Guide. If you don't need surrogate variables, then ...
written 3 months ago by Robert Castelo2.4k
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Answer: A: SVA for repeated measures design
... Hi, I would say the answer is **to include** SUBJECT.ID in the null model because, as argued by Jeff Leek, author of SVA, in this [thread](https://support.bioconductor.org/p/54719) about a similar design case, SUBJECT.ID will be used in the ultimate linear model you intend to fit to test for the ef ...
written 3 months ago by Robert Castelo2.4k

Latest awards to Robert Castelo

Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Differential expression on GSVA scores using LIMMA
Popular Question 13 months ago, created a question with more than 1,000 views. For GO term as "keytype" in GO.db
Popular Question 13 months ago, created a question with more than 1,000 views. For working with genome-wide phastCons scores
Scholar 13 months ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Popular Question 14 months ago, created a question with more than 1,000 views. For problems installing VariantFiltering package
Popular Question 14 months ago, created a question with more than 1,000 views. For Fisher-Yates algorithm for DNA shuffling ?
Popular Question 14 months ago, created a question with more than 1,000 views. For TxDb annotations for human chrM
Popular Question 15 months ago, created a question with more than 1,000 views. For TxDb annotations for human chrM
Popular Question 16 months ago, created a question with more than 1,000 views. For TxDb annotations for human chrM
Scholar 20 months ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 2.6 years ago, created an answer that has been accepted. For A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
Scholar 2.6 years ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 2.6 years 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?
Scholar 2.6 years 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 2.7 years 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 2.7 years ago, voted at least 25 times.
Scholar 2.7 years ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Scholar 2.7 years ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Scholar 3.0 years ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 3.7 years ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Appreciated 4.1 years ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?

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