User: james.dalgleish

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Posts by james.dalgleish

<prev • 14 results • page 1 of 2 • next >
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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 6 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 6 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 6 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 6 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 6 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 7 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 7 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 7 months ago by james.dalgleish30 • updated 7 months ago by Aaron Lun21k
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Comment: C: Genomic Features UCSC refseq genes "Download the knownGene table ... Error: Bad
... Is there a working github repo I can use to install it with devtools::install.github()? ...
written 8 months ago by james.dalgleish30
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Comment: C: Genomic Features UCSC refseq genes "Download the knownGene table ... Error: Bad
... I still can't seem to quite download it yet using install.packages() and the rtracklayer page (https://bioconductor.org/packages/release/bioc/html/rtracklayer.html) doesn't reflect the new version. Let me know if there is a way to access it otherwise.   ...
written 8 months ago by james.dalgleish30

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