User: Malcolm Perry

gravatar for Malcolm Perry
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40
Status:
New User
Location:
London, UK
Website:
https://github.com/Com...
Last seen:
2 months, 1 week ago
Joined:
3 years ago
Email:
m********@gmail.com

PhD Student, Computational Regulatory Genomics group, MRC Clinical Sciences Centre, London.

Posts by Malcolm Perry

<prev • 8 results • page 1 of 1 • next >
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Comment: C: plotCisTrans function in GenomicInteractions package
... No worries, thanks for the feedback! ...
written 9 weeks ago by Malcolm Perry40
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Answer: A: plotCisTrans function in GenomicInteractions package
... Hi Sarvesh, you are correct - this is reporting the number of non-zero cells, and that's what it's intended to do. I guess the terminology of interactions and interaction counts can be confusing, sorry about that. Do you think the documentation needs changing? We tried to be consistent with the term ...
written 10 weeks ago by Malcolm Perry40
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Comment: C: GenomicInteractions package read in meta data file
... This is now fixed thanks to Herve. ...
written 22 months ago by Malcolm Perry40
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Comment: C: GenomicInteractions package read in meta data file
... That will hopefully be in the next release of Bioconductor. Malcolm ...
written 22 months ago by Malcolm Perry40
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Answer: A: GenomicInteractions package read in meta data file
... At first I was surprised by this question, since we do not use data.table to import bedpe files in our package. It turns out the answer is hiding in the way S4Vectors handles metadata. The quick solution is to give mcols what it wants, which in this case in a DataFrame: mcols(mydata) <- DataFr ...
written 23 months ago by Malcolm Perry40
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Comment: C: Epigenomics RoadMap Project files now accessible via AnnotationHub
... Hi Sonali, are there any plans to add access to the raw data (ie consolidated and unconsolidated tagAlign files) through AnnotationHub? As far as I can tell, this info is not indexed in a publicly accessible way and the easiest method currently is just to parse the file names from the web server HTM ...
written 23 months ago by Malcolm Perry40
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Comment: C: Gviz highlighted regions displaying behind main plot
... Thanks Florian, this sounds ideal. I see the package has passed checks and is now available to download, I'll give it a try. ...
written 3.0 years ago by Malcolm Perry40
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Gviz highlighted regions displaying behind main plot
... Hi, I'm having issues with Gviz plotting the highlights behind the data tracks:     The code used to produce the image: library(Gviz) library(GenomicRanges) bigwig = "HCNE_density_hg19_mm10.bigWig" region = GRanges("chr3", IRanges(180436331, 182390735)) gene = GRanges("chr3", IRanges(181661 ...
gviz software error written 3.0 years ago by Malcolm Perry40 • updated 3.0 years ago by florian.hahne@novartis.com1.5k

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