User: federico.comoglio

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100
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Location:
Switzerland
Last seen:
2 years ago
Joined:
8 years, 4 months ago
Email:
f****************@gmail.com

Posts by federico.comoglio

<prev • 31 results • page 1 of 4 • next >
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Comment: A: RTCGAToolbox and miRNA-seq data - no download.
... Anyone knows how to go about this? ...
written 2.4 years ago by federico.comoglio100
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RTCGAToolbox and miRNA-seq data - no download.
... In a recent project, I used the BioC package RTCGAToolbox to conveniently fetch data from TCGA.  I now would like to download miRNA expression data for the TCGA AML patient cohort. However, while I can successfully download all other data types, miRNA expression profiles are not retrieved. A call ...
rtcgatoolbox written 2.4 years ago by federico.comoglio100
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Comment: C: Error in Gviz | IdeogramTrack
... I'm experiencing the same issue right now, from a pipeline that robustly worked over the past few months. ...
written 2.4 years ago by federico.comoglio100
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Answer: A: How can I get rather small example data from Encode sample's Chip-seq peak file
... Hi Jurat, this discussion might be of help: https://www.biostars.org/p/85063/ Federico ...
written 2.6 years ago by federico.comoglio100
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Answer: A: What tool for reads alignment are prefereble for wavClusteR input bams?
... Hi Alexandr, thank you for your interest in wavClusteR. Can you please let me know about the exact nature of your fastq data? Is this a paired-end run? In principle, the choice of the aligner does not matter as long as gaps are not allowed and reads are single-end. wavClusteR has been thoroughly te ...
written 2.6 years ago by federico.comoglio100
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Comment: C: How to interpret DNAShapeR results
... yes, agreed. ...
written 2.9 years ago by federico.comoglio100
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Comment: C: How to interpret DNAShapeR results
... Hi, Tsu-Pei was referring to a replacement for NA values that are naturally occurring at the boundaries of the genomic regions you specified, he was not suggesting to average nucleotide-resolution and base-pair-step-resolution parameters. @tsupeich We could consider adding an option to automatical ...
written 2.9 years ago by federico.comoglio100
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Comment: C: Error with wavClusteR annotateClusters function
... You can also install the package from my GitHub repository with library(devtools) install_github(repo = "FedericoComoglio/wavClusteR", ref = "devel", build_vignettes = TRUE) I would strongly advise to upgrade to R 3.3.0. Hope this helps, Federico ...
written 3.2 years ago by federico.comoglio100
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Answer: A: Error with wavClusteR annotateClusters function
... The issue is independent of your data sets (in fact the example code from ?annotateClusters is sufficient to generate it), and is due to recent changes in ggplot2. I fixed the issue and pushed the code to BioC devel (https://github.com/Bioconductor-mirror/wavClusteR). Hope this helps. Let me know. ...
written 3.2 years ago by federico.comoglio100
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Answer: A: Error with wavClusteR annotateClusters function
... Hi,       thanks for your message. The error is generated by the call below. I will look into it asap and get back to you/push the relevant changes to the devel branch. Meanwhile, can you just provide the first - say 100 - entries of the wavclusters object?   p <- ggplot( data = summaryDf, ...
written 3.2 years ago by federico.comoglio100

Latest awards to federico.comoglio

Popular Question 2.0 years ago, created a question with more than 1,000 views. For QC for Affymetrix miRNA 4.0 arrays: Error from qc/QCReport
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Failed to set session genome to ...
Scholar 3.2 years ago, created an answer that has been accepted. For A: got an error with wavClusteR package; NSBS(i, x, exact = exact, upperBoundIsStri
Scholar 4.4 years ago, created an answer that has been accepted. For A: got an error with wavClusteR package; NSBS(i, x, exact = exact, upperBoundIsStri

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