User: Rory Stark
Rory Stark • 790
- Reputation:
- 790
- Status:
- Trusted
- Location:
- University of Cambridge, Cancer Research UK - Cambridge Institute
- Last seen:
- 3 days, 1 hour ago
- Joined:
- 6 years, 6 months ago
- Email:
- r*********@cruk.cam.ac.uk
Posts by Rory Stark
<prev
• 54 results •
page 1 of 6 •
next >
0
votes
1
answer
88
views
1
answers
Answer:
A: Consensus Peakset DIffBind
... With `minOverlap=.3`, you will keep peaks called in at least 3 Control samples (peaks only called in 1 or 2 Control samples will not be included), and at least 2 of the Treated samples (peaks only called in 1 Treated sample will not be included). If you only ewant to exclude peaks called in a single ...
written 21 days ago by
Rory Stark • 790
0
votes
1
answer
115
views
1
answers
... This a a 5-year old R environment, and no longer supported.
If you download an install a recent version of R (4.0 or greater) at [https://www.r-project.org/][1], you can follow the [Bioconductor installation instructions][2] and get a workable environment fairly straightforwardly. I'd be happy to s ...
written 22 days ago by
Rory Stark • 790
0
votes
1
answer
115
views
1
answers
Comment:
C: Loading Sample Sheet in DiffBind
... Wow, are you sure? That is five years old and definitely no longer supported. What version of R are you running? Could you post the output of sessionInfo()? ...
written 22 days ago by
Rory Stark • 790
0
votes
1
answer
115
views
1
answers
Comment:
C: Loading Sample Sheet in DiffBind
... What version of `DiffBind` are you running? ...
written 23 days ago by
Rory Stark • 790
1
vote
1
answer
153
views
1
answers
... The update is now available in Bioconductor. Let me know if you have any more problems.
FYI, next month a major update of DiffBind will be released, with much greater control over model designs, contrasts, normalization, and blacklists. ...
written 6 weeks ago by
Rory Stark • 790
1
vote
1
answer
153
views
1
answers
... I have checked in the fix. It will appear in DiffBind 2.16.1 once it gets through the Bioconductor build process (usually a day or two unless there is a problem).
If you are able to install from source (ie on linux), I can send you the .tar.gz (2Mb).
Cheers-
Rory ...
written 6 weeks ago by
Rory Stark • 790
1
vote
1
answer
153
views
1
answers
... Francesca, thanks to you pointing out that it failed when you supplied the consensus peakset, but it worked when you let
`DiffBind` compute the consensus, I was able to reproduce this and find the bug. I am working on a fix now and will post here when it is available. The workaround is to do it the ...
written 6 weeks ago by
Rory Stark • 790
0
votes
1
answer
153
views
1
answers
... I'll have a look at this later this afternoon to see if I can reproduce it.
In the meantime if you are working on this now perhaps you could try the suggestion I made on the other thread? Try breaking the counting into two steps:
dbObjprova <- dba.count(dbObjprova, peaks=consensus, summits ...
written 6 weeks ago by
Rory Stark • 790
2
votes
1
answer
153
views
1
answers
... Hello Francesca-
There are a number of things that could account for this. Among other things, the consensus peakset will be different each time, which will change things a fair amount. Additionally, as you are not re-centering around summits, even if there are similar peaks in each version, they w ...
written 6 weeks ago by
Rory Stark • 790
0
votes
2
answers
164
views
2
answers
... Yes you can do this. You can divide things up using any combination
of meta-factors (Tissue, Factor, Condition, Treatment, Replicate), each of which can contain anything you like,
or by calling out any subsets of peak using masks.
Cheers-
Rory
...
written 8 weeks ago by
Rory Stark • 790
Latest awards to Rory Stark
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: [How to Save plots in R] DiffBind
Good Answer
11 weeks 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
3 months ago,
created an answer that has been accepted.
For A: [How to Save plots in R] DiffBind
Good Answer
7 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
12 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
12 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
Appreciated
16 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
Appreciated
2.2 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
Appreciated
2.4 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
Scholar
2.4 years ago,
created an answer that has been accepted.
For A: How many biological replicates needed for ChIP seq experiments?
Teacher
2.4 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
2.5 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
Appreciated
2.7 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
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: How many biological replicates needed for ChIP seq experiments?
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
3.0 years ago,
created an answer that has been accepted.
For A: How many biological replicates needed for ChIP seq experiments?
Scholar
3.0 years ago,
created an answer that has been accepted.
For A: Visualization for ChIP-seq analysis
Teacher
3.0 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
3.0 years ago,
created an answer with at least 3 up-votes.
For A: How many biological replicates needed for ChIP seq experiments?
Scholar
3.1 years ago,
created an answer that has been accepted.
For A: How many biological replicates needed for ChIP seq experiments?
Teacher
3.1 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
3.1 years ago,
created an answer that has been accepted.
For A: How many biological replicates needed for ChIP seq experiments?
Teacher
3.1 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
Appreciated
5.1 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
5.1 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
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1274 users visited in the last hour