User: Robert Castelo

gravatar for Robert Castelo
Robert Castelo2.0k
Reputation:
1,990
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Trusted
Location:
Spain/Barcelona/Universitat Pompeu Fabra
Website:
http://functionalgenom...
Twitter:
robertclab
Scholar ID:
Google Scholar Page
Last seen:
1 month, 2 weeks ago
Joined:
10 years, 1 month 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 • 237 results • page 1 of 24 • next >
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Comment: C: how to extract read alignments from reads aligning in mulitple locations
... True, using the 'use.names' argument and counting unique read identifiers i get 8.7 million reads, which is similar to the number given by STAR. thanks!! ...
written 7 weeks ago by Robert Castelo2.0k
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Comment: C: how to extract read alignments from reads aligning in mulitple locations
... Thanks a lot. I've tried out and the 'GAlignmentPairs' object 'ambiguousReads' has about 20 million pairs, however, STAR (the read mapper) tells me that there are about 9 million "reads mapped to multiple loci". Could you think of any reason responsible for this discrepancy? Maybe I'm missing some a ...
written 7 weeks ago by Robert Castelo2.0k
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how to extract read alignments from reads aligning in mulitple locations
... hi, i have a 4Gb BAM file with RNA-seq reads aligned with STAR to the hg38 version of the human genome and where, according to STAR, an important fraction of them (~25%) aligned to multiple loci. I"m interested in finding the genes that overlap these multimapping reads to have an idea of the origin ...
genomicfeatures rsamtools genomicalignments written 7 weeks ago by Robert Castelo2.0k • updated 7 weeks ago by Dario Strbenac1.3k
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Comment: C: RNAseq with technical replicates: Does it sound right?
... Before adding the raw counts across lanes, I would also do an MDS plot of all the 108 files labeled by an index of the biological sample identity and colored by lane, to assess the similarity between technical replicates from the same biological sample, they should overlap on the same spot. ...
written 8 weeks ago by Robert Castelo2.0k
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Answer: A: GSVA: questions about the bootstrap p-value
... hi, sorry for the delay in getting back to you. I'm a contributor to GSVA and not the maintainer of the package who added this feature but I'll try to answer. Indeed, bootstrapping was something added after the publication, which is the main reason why is not well described. Let me warn you that th ...
written 9 weeks ago by Robert Castelo2.0k
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Comment: C: mm10 phastCons data for use with ATACseqQC
... hi, thanks for your patience, i've edited my answer above, a 'GScores' object has now become available for phastCons60way.UCSC.mm10. cheers, robert. ...
written 11 weeks ago by Robert Castelo2.0k
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Answer: A: mm10 phastCons data for use with ATACseqQC
... hi, i'm the maintainer of phastCons100way.UCSC.hg19, this package reduces the memory requirements by rounding the phastCons scores to 1-decimal digit, i'm in the process of generating other types of GScores objects, including for instance phyloP scores with a different quantization adapted to this k ...
written 3 months ago by Robert Castelo2.0k
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Comment: C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
... hi, i think that the large user base of moderated t-tests, and the large number of publications using them, lead to more scrutiny on how these methods work. So, i'd say that if moderated t-tests would be systematically behind irreproducible results in the scientific literature, their responsibility ...
written 3 months ago by Robert Castelo2.0k
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Comment: C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
... I have edited my original answer to add two more panels to the third figure, to show the raw p-values of the classical t-test and the moderated t-test, calculated on the subset of 6 samples, as function of the raw p-values of the classical t-test calculated on the whole set of available samples (71) ...
written 3 months ago by Robert Castelo2.0k
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Answer: A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
... hi, Just in case you find this useful, when I try to show my students the difference between a classical t-test and a moderated t-test that borrows information across genes, such as the one implemented in the limma package, without showing any formulas, I show them the following three sets of plots ...
written 3 months ago by Robert Castelo2.0k

Latest awards to Robert Castelo

Scholar 10 weeks 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 3 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 3 months ago, voted at least 25 times.
Scholar 3 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 3 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 6 months ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Scholar 6 months ago, created an answer that has been accepted. For A: qpgraph's qpPCC function giving different results than cor.test()
Popular Question 16 months ago, created a question with more than 1,000 views. For [GSVA] Segfault with GSVA
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Appreciated 20 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 20 months ago, created an answer that has been accepted. For A: Network generation from adjacency matrix of zeroes and ones
Scholar 21 months ago, created an answer that has been accepted. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 21 months ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 2.3 years ago, created an answer that has been accepted. For A: retrieving phastConsScores via 'scores' from 'VariantFiltering' shows inconsist
Scholar 2.3 years ago, created an answer that has been accepted. For A: phastCons scores for GRCh38
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Bioconductor package versions
Autobiographer 2.9 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.0 years ago, created 100 posts.

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