User: Rory Stark

gravatar for Rory Stark
Rory Stark900
Reputation:
900
Status:
Trusted
Location:
University of Cambridge, Cancer Research UK - Cambridge Institute
Website:
https://www.cruk.cam.a...
Scholar ID:
Google Scholar Page
Last seen:
21 hours ago
Joined:
6 years, 9 months ago
Email:
r*********@cruk.cam.ac.uk

Principal Scientist, Computational Biology at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 69 results • page 1 of 7 • next >
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Comment: C: ChIP-seq or Cut and Run Differential Binding Analysis
... Suppose there is a region in the Treated samples that has an anomaly in the Treated control, but not in the Normal control. If you include a peak in this region because it was identified in the Normal, how can you tell if it is differentially bound in Treated if you can't rely on the Treated reads? ...
written 18 days ago by Rory Stark900
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Answer: A: Diffbind3 dba.plotMA error
... I suspect that you have an older version of `DiffBind`. The current version is 3.0.9 -- this issue was addressed in DiffBind 3.0.6. Check your version with `package.version("DiffBind")`; you can update using `BiocManager::update()`. ...
written 20 days ago by Rory Stark900
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Comment: A: Diffbind3 dba.plotMA error
... if you could send me a copy of your `Age_ATAC` object, I could have a look at what is going on. I'll also need to see the output when you call `sessionInfo()`. -Rory ...
written 21 days ago by Rory Stark900
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Answer: A: ChIP-seq normalization method when global loss of signal is expected.
... There are good discussions of these issues, with examples, in the vignettes for the Bioconductor packages `DiffBind`and `csaw`: [DiffBind Vignette][1] [csaw User's Guide][2] [1]: http://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf [2]: https://bioconductor. ...
written 22 days ago by Rory Stark900
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Comment: C: DiffBind error when calling dba.count
... If you are running `dba,count()` in the default parallel mode, it can help to run with `bParallel=FALSE` to see the full warning one at a time. When the warning is that the files are not accessible, and permission are not an issue, the most common cause is that the files are specified using relativ ...
written 5 weeks ago by Rory Stark900
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Answer: A: CHIP Seq Analysis by DiffBind Package
... The second line seems to indicate that your `SampleSheet.txt` file has at least 21602 lines, is that correct? Can you show your samplesheet? Something is incorrectly formatted, either in the sample sheet, or one (or more) of the Peak files, or both. ...
written 7 weeks ago by Rory Stark900
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Comment: C: how to retrieve binding affinity matrix in diffbind
... This issue should now be fixed in version `DiffBind_3.0.6`. You'll need to re-run the analysis from `dba.analyze()`. ...
written 8 weeks ago by Rory Stark900
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Comment: A: DiffBind 3.0: Extensive updates in Bioconductor 3.12
... I noticed the omission this morning and checked in a fix earlier today, exporting `DBA_BLACKLIST_HG38` as documented on the help page for `dba.blacklist()`. The fix will appear in the next update as `DiffBind_3_0_2` in the next day or so. In the current version, if you run with the default `blackli ...
written 9 weeks ago by Rory Stark900
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Answer: A: ChIP-seq or Cut and Run Differential Binding Analysis
... If the controls are matched -- IGG Control 1 was done in the same "batch" as Normal 1 -- you can just call peaks over the matched control. As you are doing a quantitative differential analysis with these data, there's no need to over-think the controls. The peak calling is just a step to identify p ...
written 10 weeks ago by Rory Stark900
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Answer: A: How is chip seq quantitative?
... One way to think about this in bulk ChIP-seq is that we're measuring the proportion of cells that have the protein bound (or histone mark) at each location. This is not exact, especially if there are copy number issues, but if each cell has a set number of copies of a given sequence of DNA, then see ...
written 10 weeks ago by Rory Stark900

Latest awards to Rory Stark

Autobiographer 11 weeks ago, has more than 80 characters in the information field of the user's profile.
Scholar 4 months ago, created an answer that has been accepted. For A: [How to Save plots in R] DiffBind
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
Scholar 6 months ago, created an answer that has been accepted. For A: [How to Save plots in R] DiffBind
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
Scholar 2.6 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Scholar 2.9 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Scholar 3.2 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Scholar 3.2 years ago, created an answer that has been accepted. For A: Visualization for ChIP-seq analysis
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: How many biological replicates needed for ChIP seq experiments?
Scholar 3.3 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Scholar 3.3 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit

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