User: Gord Brown

gravatar for Gord Brown
Gord Brown570
Reputation:
570
Status:
Trusted
Location:
United Kingdom
Last seen:
3 weeks, 2 days ago
Joined:
5 years, 10 months ago
Email:
g***********@cruk.cam.ac.uk

Gord is a computational biologist / bioinformatician with Cancer Research UK's Cambridge Institute.  He works on pipeline and software infrastructure development, primarily on next-gen sequencing.

Posts by Gord Brown

<prev • 113 results • page 1 of 12 • next >
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Comment: C: two factor chip with diffbind and edgeR (or DESeq2).
... Hi, One way to use input controls is via the GreyListChIP Bioconductor package.  It uses input controls to identify regions of the genome with high coverage in the input, which tend to confuse peak callers and produce a lot of spurious peaks.  You use the inputs to identify these regions, then remo ...
written 8 months ago by Gord Brown570
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Comment: C: DiffBind error with dba.count after update
... Hi, Your question is slightly confusing.  My previous comment specifically says I've commited a fix, and what version it is.  The windows devel build is failing due do dependencies, as are many other packages; nothing I can do about that.  But release is fine.  Are you still seeing errors with 2.6. ...
written 10 months ago by Gord Brown570
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Comment: C: Using HOMER called peaks in DiffBind
... Note also that in "factor" mode, HOMER produces fixed-width peaks.  For very strong peaks, that may mean that most of the reads are outside the range of the called peak (e.g. it gives you 200bp wide peaks, but the bulk of reads in a very strong peak might be more than 100bp from the centre).  If you ...
written 10 months ago by Gord Brown570
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Comment: C: Inconsistent peak width with DiffBind "summit" function
... Sometime, when we have some spare time (haha!) we should consider using PeakSplitter or similar to split distinct but nearby peaks, rather than discarding all but one.  It (probably) wouldn't be that hard to write a wrapper R package around PeakSplitter's C++ core... I'll see what Mali (the author) ...
written 10 months ago by Gord Brown570
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Answer: A: Analyzing data without replicates using DiffBind
... The second most-hated question among statistical and/or computational people (the first being do I need replicates?). How many replicates you need depends on two parameters: 1) What effect size are you trying to detect, between the experimental groups?  (For example, is a fold change of 10:1 all y ...
written 10 months ago by Gord Brown570
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Answer: A: Analyzing data without replicates using DiffBind
... Hi, Without replicates, you cannot hope to test meaningfully for statistically significant differences, with DiffBind or anything else. The DiffBind vignette describes two approaches to analysis.  You might look into an "occupancy" analysis, which allows you to, for example, draw Venn diagrams sho ...
written 11 months ago by Gord Brown570
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Answer: A: DiffBind error with dba.count after update
... Hi, I've commited a fix to release and devel, so you should see DiffBind 2.6.1 and 2.7.1 as soon as it gets built.  Sorry for the inconvenience.  - Gord ...
written 11 months ago by Gord Brown570
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Answer: A: Error When using dba.count() in DiffBind
... Hi, I've commited a fix to release and devel, so you should see DiffBind 2.6.1 and 2.7.1 as soon as it gets built.  Sorry for the inconvenience.  - Gord ...
written 11 months ago by Gord Brown570
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Comment: C: Error When using dba.count() in DiffBind
... I'll post a comment as soon as I check in a fix.   ...
written 11 months ago by Gord Brown570
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Comment: C: DiffBind error with dba.count after update
... Hi, Yes, it's broken.  I'll check in a fix ASAP. The rules for registering native routines were tightened up a bit, and the one used by dba.count wasn't (isn't) registered properly.  I'l. post as soon as I check in the fix.  Sorry about that. ...
written 11 months ago by Gord Brown570

Latest awards to Gord Brown

Centurion 17 months ago, created 100 posts.
Scholar 17 months ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Scholar 18 months ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Scholar 3.0 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Counting Raw Reads with DiffBind
Scholar 3.5 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Autobiographer 3.6 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 3.9 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals

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