User: Gord Brown

gravatar for Gord Brown
Gord Brown590
Reputation:
590
Status:
Trusted
Location:
United Kingdom
Last seen:
2 months, 3 weeks ago
Joined:
6 years, 5 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 • 116 results • page 1 of 12 • next >
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Comment: C: Diffbind: Using bigwig tracks in place of bam files
... DiffBind won't accept coverage files, normalized or not, but if you can convert them to count tables, then you should be able to run DiffBind on it. Rory recently added a comment on using DiffBind with counts directly: https://support.bioconductor.org/p/119168/#119355 Given that the counts will no ...
written 11 weeks ago by Gord Brown590
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Answer: A: Diffbind: Using bigwig tracks in place of bam files
... No, DiffBind (and DESeq2 and EdgeR) require (un-normalized) counts, not coverage files. The rationale (for DESeq2 specifically) is discussed here: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-un-normalized-counts Sorry... - Gord ...
written 11 weeks ago by Gord Brown590
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Comment: C: Warning in "countReads" [Warning message: In .Seqinfo.mergexy(x, y) : The 2 comb
... The genomes have to match exactly.  In particular, UCSC and Ensembl genomes differ, in addition to chromosome naming, in tiny ways that almost never matter, until a situation like this.  As you've already found, just changing the chromosme names isn't enough (though you can get away with it sometime ...
written 5 months ago by Gord Brown590
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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 16 months ago by Gord Brown590
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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 18 months ago by Gord Brown590
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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 18 months ago by Gord Brown590
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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 18 months ago by Gord Brown590
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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 19 months ago by Gord Brown590
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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 19 months ago by Gord Brown590
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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 19 months ago by Gord Brown590

Latest awards to Gord Brown

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Counting Raw Reads with DiffBind
Scholar 2.1 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Centurion 2.1 years ago, created 100 posts.
Scholar 2.1 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Scholar 3.6 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Counting Raw Reads with DiffBind
Scholar 4.2 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Autobiographer 4.3 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 4.6 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals

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