hey everyone,
I'm performing ChIP-Seq analysis using diffbind,
after doing:
> dba.count(peaksets, summits=250)
I would like to get the binding affinity Matrix into a text file.
help
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I was wondering how Diffbind deals with the problem of using multiple blocking factors (let's say, age, gender and postmortem delay). If there is...I was wondering how Diffbind deals with the problem of using multiple blocking factors (let's say, age, gender and postmortem delay). If there is a...at the same time, what's the best way of doing it? Should I correct this manually myself somehow, or …
updated 5.0 years ago • melnuesch
MACS2 considering matched inputs. To perform the differential binding analysis, I finally ran the DiffBind package on those data.
When I created the DiffBind dba object with :
<pre>
<em>Expe_K4Me1 <- dba(sampleSheet=Samples_K4Me1...img alt="" src="http://i.imgur.com/BWeer4w.jpg" style="height:255px; width:400px"/>
Before running DiffBind, I checked the overall concordanc…
updated 10.4 years ago • Pierre-François Roux
Hello!
I met a problem when I tried to construct DBA object with dab() in Diffbind.
This is my sampleSheet.
![enter image description here][1]
And the command
dbaNSD <- dba(sampleSheet="sampleSheet.csv...Hello!
I met a problem when I tried to construct DBA object with dab() in Diffbind.
This is my sampleSheet.
![enter image description here][1]
And the command
dbaNSD &l…
updated 4.9 years ago • ahua217
Hi, I am trying to help a labmate who is using DiffBind to do a PCA analysis on some ATAC-seq data that she generated. I have experience with PCA but not with this specific...Hi, I am trying to help a labmate who is using DiffBind to do a PCA analysis on some ATAC-seq data that she generated. I have experience with PCA but not with this specific software. How can we retrieve the PCA loadings/eige…
updated 4.5 years ago • Spendlove
Hello,
I am trying to understand DiffBind in order to use it for my ATAC-seq data analysis and find differential open chromatin sites. could you please explain
updated 9.6 years ago • simonjean434
Hi Rory Stark,
I am a little confused about the following questions regarding the use of DiffBind:
How does DiffBind handle normalization? Does it use the raw counts from BAM files? Are the total reads counts used...as we analyze RNA-seq read counts, which require raw read counts as input?
Is it possible to use DiffBind without spike-in normalization?
Thanks in advance
updated 2.7 years ago • skyyks123
30:49 +0530
To: Rory Stark
<rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>>
Subject: DiffBind Questions
Dear Rory,
We have been using DiffBind on our Chip-seq data. I would like to
know, to see the correlation replications
paolo
2012/7/31 Gordon Brown <gordon.brown at="" cancer.org.uk="">:
> Hi, Paolo,
>
> DiffBind uses quite a lot of memory for the dba.count step, because
it loads
> the whole data file into memory. (In hindsight...C:/Documents and Settings/pkunderfranco/Documenti/Data
/ChIP-seq
>>> Roberto/Analisi_PK/DiffBind/H3K27me3/")
>>
&am…
How to correct this error `` More fragment sizes than libraries `` in DiffBind Package ? What does that means
updated 8.4 years ago • ZheFrench
Enter the body of text here
Code should be placed in three backticks as shown below
```#DiffBind version 3.2.4
library(DiffBind)
getwd()
setwd("/Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC...Screening.csv", header=TRUE, sep=",")
names(samples)
samples
#read peaksets using the "dba" DiffBind function and creates a DBA object
#The peak score (prior to counting reads) i…
updated 4.2 years ago • mtsompana
So I am using DiffBind to create a count matrix as summarizedExperiment and then running this through DESeq2 and I was wondering about...So I am using DiffBind to create a count matrix as summarizedExperiment and then running this through DESeq2 and I was wondering about ways to filter for specific baseMean ranges within this data? My script looks like the following:
<pre>
library("DESeq2…
updated 7.2 years ago • rbronste
Stark
<rory.stark@cancer.org.uk<mailto:rory.stark@cancer.org.uk>>
Subject: Question concerning Diffbind
Resent-From: Rory Stark
<rory.stark@cancer.org.uk<mailto:rory.stark@cancer.org.uk>>
Dear Dr. Stark
I am a graduate...student at POSTECH and have a question concerning
DiffBind.
I have multiple samples of different condition but do not have any
replicate nor co…
updated 12.7 years ago • Rory Stark
Hi!
I'm calling peaks and later comparing conditions for a Cut&Run dataset and would like to know what is the recommended approach on using DiffBind.
I have a Control, Treatment (both in triplicates) and relevant IgG for both the conditions. Here in lies my need for a...for a Cut&Run dataset and would like to know what is the recommended approach on using DiffBind.
I have…
updated 7 months ago • Harish
Hi,
I'm using Diffbind to analysis differential binding H3K27Ac histone ChIP-seq site!
I'm curious whether I can find all the relative...Hi,
I'm using Diffbind to analysis differential binding H3K27Ac histone ChIP-seq site!
I'm curious whether I can find all the relative site
updated 7.0 years ago • woongjaej
I have some questions about Diffbind analysis when there are multiple groups to be compared. For example, if we have group1, group2 and group3 and wish...I have some questions about Diffbind analysis when there are multiple groups to be compared. For example, if we have group1, group2 and group3 and wish to
updated 5.0 years ago • Vince Schulz
51:49 +0100
To: Rory Stark
<rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>>
Subject: DiffBind and paired end data
Dear Dr. Stark,
I had the pleasure to attend ("back then in 2013") to the presentation
you gave at the...EBI Advanced Course for RNA-seq and ChIP-seq, where
you introduced DiffBind and its usage examples.
Now I moved from IMB - Mainz and I am working in…
Hi folks,
I am new to ChIP-seq analysis hence this may be a basic question. I want to use DiffBind to get peak summits, but after running `dba.count` with my own peaks, I find the number of peaks has decreased. Is this...Hi folks,
I am new to ChIP-seq analysis hence this may be a basic question. I want to use DiffBind to get peak summits, but after running `dba.count` with my own peaks, I f…
updated 3.6 years ago • soyabean
Sorry for the mundane question, but I think I used to be able to change the color of heatmaps in Diffbind using col = , and now that doesnt seem to work, Now I get the following error:
> plot(samples\_final, col ="blues")
Error
updated 8.2 years ago • andrew.gehrke
Hi wondering how I can use the following DESeq2 logic within the framework of DiffBind for calling differential peaks and looking at multiple interactions:
<pre>
to look at interaction--
dds<-DESeqDataSetFromMatrix
updated 4.8 years ago • rbronste
Dear Bioconducters
I am running ChIPseq analyses via DiffBind 2.2.12 using DESeq option.
As indicated in the vignette I run dba.analyze() and the extract the results with dba.report
p style="direction: ltr;">Hi,</p>
<p style="direction: ltr;">We are trying to use diffBind and are puzzled by the scale on our correlation matrices. In one of our datasets the correlation goes between 0.9
updated 9.9 years ago • eli7javasky
Hello! I am performing a differential analysis on ATAC-seq data in DiffBind. I would like to know if it is possible to plot ellipses around a PCA plot. I generated my plots with the following code
updated 3.3 years ago • Lisa
Hello,
I tried DiffBind (v3.0.9) to find DE binding sites from ChIP-seq data. When I used "dba.normalize" with "background=TRUE". It ended up with...Hello,
I tried DiffBind (v3.0.9) to find DE binding sites from ChIP-seq data. When I used "dba.normalize" with "background=TRUE". It ended up with this error:
```r
DB = dba.normalize(DB, normalize=DBA_NORM_NATIVE, background=TRUE)
Gene…
updated 4.8 years ago • Victor
div class="preformatted">Hi, I'm Ken Tanaka.
I'm currently interested in analyzing the DiffBind analysis by using
the
ChIP-seq data from Th2 immune cell samples.
To be more specific, I would like to analyze this...GSE28292) by
using DiffBind analysis.
I have questions regarding the dba.count().
When I execute the dba.count(), it crashes.
The bed data which I...from the problems
regarding t…
mask=1:29, label = DBA_CONDITION, labelSize = 0.65, contrast = 19)
Being very new to Diffbind, I would really appreciate if someone could confirm that it is correct. Also, if my code is correct, could someone provide
updated 6.6 years ago • Helene
Dear all,
is there any way to change the dimension of the PCA plot is the DiffBind package? How can I change label size in this plot?
Thanks
updated 5.8 years ago • bony.dekumar
Hi everyone, I am trying to use DiffBind to process an unusually large dataset (101 ATAC-seq samples). Is there a way to construct the dba object using `dba()` in
updated 2.4 years ago • Shashank
nbsp;
Hello,
I was looking at previous posts about MACS2 peak files and read shift before DiffBind to match MACS2 settings. However, I am still a bit confused about right steps to take. This is my work strategy:
1)  ...shift 25b from 3' ->5' and after that set read length = 50)
2) Load NarrowPeaks files in DiffBind and obtain consensus peakset (for all replicates from…
data similar to ChIP-Seq) after degradation of my protein of interest. I am currently using Diffbind in combination with DESeq2 method of dba.analzye() but diffbind provides so many different options for dba.normalize...when using Option 1 vs Option 2 in dba.normalize().
Thank you!
```r
#Importing the the table for diffbind containing all the necessary files, names, and locations
CTCF_narrowp…
updated 4.9 years ago • Monica
Hi Rory Stark，
DiffBind normalization based on the total reads of a bam file by default, right? And the final results of DiffBind: Conc_Resistant
updated 2.6 years ago • skyyks123
Would you please help? Thank you so much!
https://bioconductor.org/packages/devel/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf
Page 22 the manual explains this plot but I am still not sure.
![enter image description here
updated 2.4 years ago • Chris
Hi ,
I am currently working on 12 ATAC-Seq samples using Diffbind. Following the tutorial, the first step involved generating a dba object and setting the minoverlap parameter...Hi ,
I am currently working on 12 ATAC-Seq samples using Diffbind. Following the tutorial, the first step involved generating a dba object and setting the minoverlap parameter to...A, but when I go back to check the input…
I am using diffbind to find differential peaks between different samples obtained in different conditions. The manual says that...I am using diffbind to find differential peaks between different samples obtained in different conditions. The manual says that dba.analyze
updated 9.0 years ago • onkarnath89
Hi,
I was trying to use DiffBind to analyze my ATAC-Seq data. When I call the dba.count() function, I got the following error message:
Error: Error processing...errors in user code
2: "croi\_count\_reads" not resolved from current namespace (DiffBind)
3: "croi\_count\_reads" not resolved from current namespace (DiffBind)
4:&am…
my hair out trying to figure out how to resolve an issue I am having with reading peaksets into Diffbind. The peaks files I am trying to use are .narrowPeak files derived from MACS2. It is my understanding that Diffbind is...binary operator"
```
I have no "scoreCol" column in my sample sheet. I wondered whether maybe Diffbind was having trouble with the .narowPeak files so substituted thes…
updated 2.6 years ago • os306
DiffBind"),
peak.caller="macs", sampID="WT2017",tissue="BM B cells",
factor="WT", replicate=1)
dp.K4 <- dba.peakset(dp.K4,
peaks=system.file...2036_K4_peaks.xls", package="DiffBind"),
peak.caller="macs", sampID="WT2036",tissue="BM B cells",
factor="WT",replicate=2)
dp.K4 <- …
to extract such data for specific windows at some point in the analysis. I am asking as I never used DiffBind before and I do not know at which point such control samples are used in the analysis.
Thanks in advance
updated 2.4 years ago • agata17
9.263 . 9.263
1.709270e+00 2.493753e-02 0
>---------------
>
>When DiffBind tries to normalise the score based on the width of the
peak,
>it comes out as N/0, which R shows as infinity. Things go...downhill
from
>there. This is a bug in DiffBind (if the width is zero, we should
just
>make it 1, for example). But in the meantime, to work a…
updated 11.7 years ago • Rory Stark
again, sorry lots of questions at the moment,
I would like to replicate the following function from diffBind
<pre>
> dba.plotMA(tamoxifen, bXY=TRUE) </pre>
However I don't know how to retrieve this data, in Deseq2 I believe it would
Dear DiffBind developers/users,
I have runned my histone ChIP-seq differential analysis using DiffBind some months ago. Back then...Dear DiffBind developers/users,
I have runned my histone ChIP-seq differential analysis using DiffBind some months ago. Back then I saved my output from **dba.analyze(test_contrast, method=DBA_ALL_METHODS)** as an **.RDS file**. At that point I also used DiffBi…
updated 2.2 years ago • M.Vukic
<div class="preformatted">Dear list,
--I'm trying to use Diffbind package to analyze some samples from a
ChIP
seq experiment.
--I created a .csv samplesheet with the following fields and which
samples
to analyze:
SampleID Tissue Factor Condition Replicate Reads Control Peaks
Chip_K27.1+ Neural K27 Responsive 1 Chip_K27.BED Input_K.BED
Chip_K27.BED
Chip_K27.2+ Neural K27 Responsiv…
I got a strange PCA (for DiffBind version 2.12.0 which is not the newest version).
The first PC explains 90% of the variance. Nevertheless, the distances...which explains a much larger percentage of variance).
How to make sense of it?
```r
library(DiffBind)
design_i <- read.csv("design_vs_Input.csv")
dbObj_i <- dba(sampleSheet = design_i)
dbObj_i <- dba.count…
updated 4.8 years ago • Sam
DiffBind is wonderful that can cluster my H3K27ac ChIP-Seq samples very well as below fig1. However, is there any method or other
updated 10.3 years ago • Gary
this and make the unzipped directory your current
directory,
instead of system.file("extra", package="DiffBind"), the vognette
should
run, including the call to dba.count.
Cheers-
Rory
On 20/08/2013 17:46, "Beh Ching Yew" <behchingyew...at="" gmail.com=""> wrote:
>Dear Rory,
>
>I am currently looking into DiffBind for my Chip-Seq data analysis.
>Would apprecia…
Hello,
This question is in regards to using DiffBind (or DESeq2) with multiple samples.
Currently, I am using DiffBind (version 2.8.0) to find differential peaks from ATAC
updated 7.0 years ago • duvaller
Hello all,
I am trying to use DiffBind on my ATAC seq data. However, the code in the manual uses ChIP seq data. Would you advise me on what to do for a learner...Hello all,
I am trying to use DiffBind on my ATAC seq data. However, the code in the manual uses ChIP seq data. Would you advise me on what to do for a learner? Thank
updated 2.6 years ago • Chris
It seems DiffBind run everything on top of dba objects. But all peak data are stored as GRanges objects in my workflow. How to make the
updated 9.2 years ago • xulong.wang
Hi,
I'm having an issue during the 'Counting reads' and 'Performing the differential analysis' step. I am receiving these messages/errors:
## Performing the differential analysis # .... [TRUNCATED]
Warning message:
In data(Condition_counts) : data set ‘Condition_counts’ not found
OR
## Performing the differential analysis ##
> Condition <- dba.ana…
updated 6.6 years ago • ryclb22
<div class="preformatted">Hi Anna-
Before running DESeq, DiffBind sets all counts to a minimum value of
1.
Not sure if that is in the documentation anywhere!
Cheers-
Rory
On 11/09/2013 17:47, "Anna Poetsch" <anna.poetsch at="" cancer.org.uk="">
wrote:
>Dear Rory,
>
>I attended the class about ChIP-Seq data analysis at EBI recently,
where
>you introduced…
<div class="preformatted">Hi Rong-
You are correct that the peak merging logic results in wider peak
areas
that may incorporate multiple binding sites and/or make it more
difficult
to determine the precise binding site. This is true of the peak
calling
step as well. In our experience, the scientific questions we are
actually
asking do not require the precise binding location in the differe…
52, "Goutham atla" <goutham.atla at="" gmail.com=""> wrote:
>Dear Dr. Stark,
>
>I am using DiffBind for Chip-Seq data analysis. I have biological
>replicates between two conditions.
>
>
>SampleID,Tissue,Condition...and Conditions ), should I perform any
>normalization of the data ( MANorm etc ) ? Or The DiffBind will take
>care…
updated 11.9 years ago • Rory Stark
I have a question about the DiffBind program. I am an immunologist and have recently started to use R for data analysis. Now, I am trying to analyze our ChIP...seq data using DiffBind to identify genomic regions that are commonly or differentially bound by one transcription factor and its mutant...nbsp;
I have a total of 4 samples, two replicates for each condition.
I used R: 3.1.3 version and …
updated 10.5 years ago • ruka.setoguchi
events between WT and mutant cells for both histone modifications.
Can I analyze this data using DiffBind even though I don't have replicates?
Thank you! 
updated 7.9 years ago • Hesh
to clarify some technical details which I’ve been trying to search for in the documentations for DiffBind, but seem to have missed it. I am interested to know the details of how the correlation of occupancy (using peak caller
updated 10.9 years ago • meisan406
Is there a way to grep the percentages PC1 and PC2 variance explained from dba.plotPCA in diffbind or chipQC ?
In my pca plot PC1 and PC2 numbers seem inversed . I'd like a way to recompute them from scratch (as asked 
Hi,
I would like to use dba.plotVolcano function in DiffBind, but R 3.3.3 cannot find it. In addition, I found that options of bNotDb, bGain, and bLoss for dba.report don’t work in...DiffBind 2.2.12. I guess that it is because my DiffBind is not the last version, i.e. 2.4.8. However, when I install DiffBind again...for an HTML browser interface to help.
Type 'q()' to quit R.
…
updated 8.1 years ago • Gary
Hi,
I have been working with Diffbind to identify differential binding of H3K9me3 due to ethanol treatment. We are using both males and females, and initially
updated 19 months ago • erbrocato
<div class="preformatted">Hi,
Is there a way to use DiffBind to analyse time course data?
I have sample and control replicates at five different time points and
I would like to...div class="preformatted">Hi,
Is there a way to use DiffBind to analyse time course data?
I have sample and control replicates at five different time points and
I would like
updated 11.1 years ago • enricoferrero
Recent ...
Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh.
```
> z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE)
> class(counts(z))
[1] "DelayedMatrix"
att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me.
```
> example(read10xCounts)
rd10xC> # Mocking up some 10X genomics output.
rd10xC> ex…
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teamardigen
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Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
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dan.gatti
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I am, but perhaps I'm not understanding how it should work.
> sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
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Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
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