User: Rory Stark
Rory Stark • 490
- Reputation:
- 490
- Status:
- Trusted
- Location:
- University of Cambridge, Cancer Research UK - Cambridge Institute
- Last seen:
- 3 months, 1 week ago
- Joined:
- 4 years, 7 months ago
- Email:
- r*********@cruk.cam.ac.uk
Posts by Rory Stark
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... The DiffBind package in Bioconductor creates a read count matrix from peak calls and aligned reads. ...
written 3 months ago by
Rory Stark • 490
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... I'm not sure how two peaks could be considered "similar" if their locations are several kb apart? We usually think of peaks being the same in replicates if their coordinates at least overlap.
That said, a very easy way to get pearson or spearman correlation values is to read all the peaksets into t ...
written 4 months ago by
Rory Stark • 490
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Comment:
C: question about DiffBind
... This is telling `DiffBind` to look in a specific directory within the package installation for the samplesheet file. This is very non-standard -- it only looks there for the example samplesheet as this is part of the installation itself. The specific error is that the first peak file doe not exist w ...
written 4 months ago by
Rory Stark • 490
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... Control reads, such as those from an Input sample, are optional in DiffBind, so you can just leave out the control column in the sample sheet. ...
written 5 months ago by
Rory Stark • 490
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... I have certainly see this level of differentially Some questions:
- Do you expect the conditions to change the open chromatin landscape
quite a bit?
- How are the differential sites divided between
the two conditions? Do they mostly show increases in one
condition, or are there many ch ...
written 7 months ago by
Rory Stark • 490
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... Has this been resolved?
You shouldn't need to specify the genome as DiffBind takes the chromosome names directly from the peak files, so if they are consistent it should work. However there was a bug at some point that impacted this in certain cases. What version of DiffBind are you using?
Alterna ...
written 7 months ago by
Rory Stark • 490
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... Disclosure: I am the author of `DiffBind`, a differential binding analysis tool.
Interestingly, the tools you are considering are not the ones most often used to derive results in the published literature. `MACS` + `DiffBind` is by far the most widely used combo for experiments with multiple biolog ...
written 9 months ago by
Rory Stark • 490
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... Can you confirm which version you are using from `sessionInfo()`?
I'm limited in what I can do without examining the object, but here's a few things to look at.
Something is going on in counting the A sample peaks. Look at them un-normalized (`bNormalized=FALSE`). If they are all 1 then nothing is ...
written 9 months ago by
Rory Stark • 490
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... Hello, I am the author of `DiffBind`.
1) There are a number of things that could account for the A-B differences. You say all the shifts are in one direction, which I assume means that the fold-changes of all the differentially bound (DB) sites have the same sign? It may be instructive to look at t ...
written 9 months ago by
Rory Stark • 490
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... The most obvious answer would be that there may not be any significantly deferentially bound peaks in your experiment. This could be due to the biology (nothing is changing) or be related to the experimental design. For example, the experiment could be underpowered, mostly likely due to not having e ...
written 10 months ago by
Rory Stark • 490
Latest awards to Rory Stark
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5 months ago,
created a post with more than 5 votes.
For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
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5 months ago,
created an answer that has been accepted.
For A: How many biological replicates needed for ChIP seq experiments?
Teacher
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For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Teacher
7 months 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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9 months ago,
created a post with more than 5 votes.
For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Scholar
9 months ago,
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For A: How many biological replicates needed for ChIP seq experiments?
Teacher
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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
13 months ago,
created an answer that has been accepted.
For A: How many biological replicates needed for ChIP seq experiments?
Scholar
13 months ago,
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For A: Visualization for ChIP-seq analysis
Teacher
13 months 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
13 months ago,
created an answer with at least 3 up-votes.
For A: How many biological replicates needed for ChIP seq experiments?
Scholar
13 months ago,
created an answer that has been accepted.
For A: How many biological replicates needed for ChIP seq experiments?
Teacher
13 months 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
13 months ago,
created an answer that has been accepted.
For A: How many biological replicates needed for ChIP seq experiments?
Teacher
13 months 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
Appreciated
3.2 years ago,
created a post with more than 5 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: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
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4.1 years ago,
created a question with more than 1,000 views.
For ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
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4.5 years ago,
created a post with more than 5 votes.
For ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
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