User: Rory Stark
Rory Stark • 460
- Reputation:
- 460
- Status:
- Trusted
- Location:
- University of Cambridge, Cancer Research UK - Cambridge Institute
- Last seen:
- 1 week, 2 days ago
- Joined:
- 4 years, 4 months ago
- Email:
- r*********@cruk.cam.ac.uk
Posts by Rory Stark
<prev
• 21 results •
page 1 of 3 •
next >
0
votes
1
answer
159
views
1
answers
... The DiffBind package in Bioconductor creates a read count matrix from peak calls and aligned reads. ...
written 20 days ago by
Rory Stark • 460
0
votes
1
answer
113
views
1
answers
... 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 weeks ago by
Rory Stark • 460
0
votes
1
answer
125
views
1
answers
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 weeks ago by
Rory Stark • 460
5
votes
1
answer
211
views
1
answers
... 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 12 weeks ago by
Rory Stark • 460
3
votes
1
answer
385
views
1
answers
... 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 4 months ago by
Rory Stark • 460
0
votes
1
answer
265
views
1
answers
... 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 4 months ago by
Rory Stark • 460
5
votes
1
answer
753
views
1
answers
... 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 6 months ago by
Rory Stark • 460
0
votes
1
answer
402
views
1
answers
... 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 6 months ago by
Rory Stark • 460
1
vote
1
answer
402
views
1
answers
... 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 6 months ago by
Rory Stark • 460
0
votes
1
answer
294
views
1
answers
... 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 7 months ago by
Rory Stark • 460
Latest awards to Rory Stark
Appreciated
12 weeks 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
12 weeks ago,
created an answer that has been accepted.
For A: How many biological replicates needed for ChIP seq experiments?
Teacher
12 weeks 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
4 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
6 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
6 months ago,
created an answer that has been accepted.
For A: How many biological replicates needed for ChIP seq experiments?
Teacher
6 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
10 months ago,
created an answer that has been accepted.
For A: How many biological replicates needed for ChIP seq experiments?
Scholar
10 months ago,
created an answer that has been accepted.
For A: Visualization for ChIP-seq analysis
Teacher
10 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
10 months ago,
created an answer with at least 3 up-votes.
For A: How many biological replicates needed for ChIP seq experiments?
Scholar
10 months ago,
created an answer that has been accepted.
For A: How many biological replicates needed for ChIP seq experiments?
Teacher
10 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
10 months ago,
created an answer that has been accepted.
For A: How many biological replicates needed for ChIP seq experiments?
Teacher
10 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
2.9 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
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
Popular Question
3.8 years ago,
created a question with more than 1,000 views.
For ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
Appreciated
4.3 years ago,
created a post with more than 5 votes.
For ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 820 users visited in the last hour