User: james.dalgleish

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Posts by james.dalgleish

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Comment: C: "Packages required but not available." rtracklayer in OSX is not available to CR
... Might be an idea for the future. My code is fairly well documented and has good vignettes at this point. It took a LOT of work to get CRAN to take it, though. I imagine the process for getting accepted on Bioconductor is very difficult, like CRAN. Thanks for the insights into the mechanics. That's p ...
written 4 weeks ago by james.dalgleish30
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"Packages required but not available." rtracklayer in OSX is not available to CRAN, resulting in errors for downstream dependencies.
... So, I'm attempting to update my CRAN package and it depends on several other packages. What I notice is that many packages fail with errors on OSX checks due to Bioconductor packages not being visible when CRAN checks are run. I guess I'm posting first to Bioconductor because I know that the communi ...
variantannotation rtracklayer genomicranges s4vectors summarizedexperiment written 4 weeks ago by james.dalgleish30 • updated 4 weeks ago by Steve Lianoglou12k
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Comment: A: Old jmosaics working package
... Is there a replacement that does something similar? I've never seen anything quite like it previously. ...
written 17 months ago by james.dalgleish30
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Old jmosaics working package
... I've had a hard time finding it, but is there a jmosaics package that is version 1.1.0? I've been trying to find it and had old code that required it's use for chipseq. http://www.bioconductor.org/packages//2.13/bioc/html/jmosaics.html The package binary (zip) listed here doesn't actually contain a ...
jmosaics written 17 months ago by james.dalgleish30
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Answer: A: Using massifquant for peak detection of generic matrix data?
... So, the author provided an answer when I posed the question on the github site. I think this may be useful to many, so I'll post it here: " It is possible to phrase your question in terms of density estimation though. I've tried to illustrate with the following toy example: library(yamss) librar ...
written 17 months ago by james.dalgleish30
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Comment: C: Using massifquant for peak detection of generic matrix data?
... Can you provide an example of how that would work? creating a new CMSraw object from a datatable is not straightforward. ...
written 17 months ago by james.dalgleish30
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Using massifquant for peak detection of generic matrix data?
... Is it possible to use massifquant for peak detection of non-MS data, but rather just finding traces that might look like MS peaks in a large matrix (150000x150000), for instance? ...
xcms kalman centwave yamss written 17 months ago by james.dalgleish30
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Comment: C: two factor chip with diffbind and edgeR (or DESeq2).
... Essentially, you recommend dropping input controls entirely then? ...
written 18 months ago by james.dalgleish30
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Comment: C: two factor chip with diffbind and edgeR (or DESeq2).
... Thanks for the response. Doesn't edgeR expect count data? Wouldn't it be better to provide counts using bedtools subtract using an input control, feed that into a counts matrix, then perform standard edgeR analysis?  Perhaps FC is a valid way to go about it. I'm open to that idea, but it would seem ...
written 18 months ago by james.dalgleish30
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two factor chip with diffbind and edgeR (or DESeq2).
... Is it somehow possible to do a chipseq experiment with two factors (treatment, no treatment), (antibody of interest, control Ig antibody)? I believe that one could do this with edgeR utilizing count data from chipseq and creating a DGEList with the group representing each individual chipseq run, and ...
edger diffbind written 18 months ago by james.dalgleish30 • updated 18 months ago by Aaron Lun24k

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