User: Gord Brown

gravatar for Gord Brown
Gord Brown590
Reputation:
590
Status:
Trusted
Location:
United Kingdom
Last seen:
7 months, 3 weeks ago
Joined:
6 years, 11 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 2 of 12 • next >
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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 2.0 years ago by Gord Brown590
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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 2.0 years ago by Gord Brown590
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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 2.0 years ago by Gord Brown590
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Comment: C: Error When using dba.count() in DiffBind
... Turns out dba.count *is* broken on R 3.4.2.  I'll get right on that, shall I? ...
written 2.0 years ago by Gord Brown590
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Comment: C: Error When using dba.count() in DiffBind
... Hi, The output may change a tiny bit.  For example, my counting code counts a read if it overlaps a peak by half its length, while summarizeOverlaps may use a slightly different rule (I haven't checked in detail).  But I'm confident it won't change the final results noticably. The version of R and ...
written 2.0 years ago by Gord Brown590
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Answer: A: Error When using dba.count() in DiffBind
... Hi, "croi_count_reads" is a C function for counting.  Most likely your copy of DiffBind is not correctly installed.  Try reinstalling it.  Or use the "bUseSummarizeOverlaps" option to use an alternate counting function. ...
written 2.0 years ago by Gord Brown590
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Answer: A: Error with dba.count function code
... Hi Try changing the column name from "BamReads" to "bamReads".  It's case sensitive, and yes, it's inconsistent with the other column names... Cheers,  - Gord ...
written 2.1 years ago by Gord Brown590
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Comment: C: Diffbind: edgeR or DESeq2 ?
... Hi, I recommend filtering before peak calling.  Peak callers such as MACS2 do use the input to filter out peaks that are also present in input, but they do not cope particularly well in regions where the input is particularly noisy, and tend to call a lot of spurious peaks.  (That's sort of the who ...
written 2.1 years ago by Gord Brown590
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Answer: A: Error with dba.count function
... Hi, Diffbind is sensitive to filename suffixes.  Bam files must end with ".bam".  In hindsight probably a bad design choice.. seemed like a good idea at the time... Cheers,  - Gord ...
written 2.1 years ago by Gord Brown590
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Comment: C: DiffBind consensus peak help
... Changing the order of lines in the sample sheet will change the order of the (auto-generated) comparisons (i.e. control vs treatment as opposed to treatment vs control) (please confirm or correct, Rory).  But if that's changing what shows up as significant, sounds like something's wrong.  Rory?  Any ...
written 2.2 years ago by Gord Brown590

Latest awards to Gord Brown

Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Counting Raw Reads with DiffBind
Scholar 2.5 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Centurion 2.5 years ago, created 100 posts.
Scholar 2.6 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Scholar 4.0 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Counting Raw Reads with DiffBind
Scholar 4.6 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Autobiographer 4.7 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 5.0 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals

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