are deferentially bound between two sample groups. I've read through the [Bioconductor manual for Diffbind](http://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf), but I do not understand...knowledgeable in programming languages. I'm wondering how much I need to learn to be able to perform Diffbind on my ChIP-seq datasets.
Are there any Diffbind tutorials/guides …
Order by: Relevance
Hello Rory,
Thanks for the Diffbind package, it makes DB analysis very easy.
However, I have the following question: How does DiffBind handle Input samples...Hello Rory,
Thanks for the Diffbind package, it makes DB analysis very easy.
However, I have the following question: How does DiffBind handle Input samples and how does it compare condition B with condition A? For example, I …
updated 5.0 years ago • liruiradiant
Hi,
I can run DiffBind well before. However, after I updated R 3.2.0, R RStudio 0.99.441, and DiffBind 1.14.4, the DiffBind cannot be used anymore...nbsp;
there is no package called ‘GO.db’
Error: package or namespace load failed for ‘DiffBind’
I have install GO.db & DiffBind many times, but it doesn't work. Could you give me a help? Many thanks.
Gary
<img al…
Hi,
I am using DiffBind to assess the H3K27me3 chipseq binding differences between two conditions. I am using default settings. I would...Hi,
I am using DiffBind to assess the H3K27me3 chipseq binding differences between two conditions. I am using default settings. I would like to visualize differentially bound regions in IGV/UCSC Genome Browser. I have generated RPM normali…
updated 8.4 years ago • akdess
Normally, DiffBind is used for ChIP-seq data, but I've seen it used for ATAC-seq as well. I don't see any issues with that. MACS can be used for...If the reads are adjusted for peak calling, what happens when I then pass the peaks and the BAMs to DiffBind? Wouldn't DiffBind quantify the peaks incorrectly since the BAMs and peaks do not really represent the same data
updated 7.7 years ago • igor
namespace (DiffBind)
13: "croi_count_reads" not resolved from current namespace (DiffBind)
14: "croi_count_reads" not resolved from current...namespace (DiffBind)
15: "croi_count_reads" not resolved from current namespace (DiffBind)
16: "croi_count_reads" not resolved from current...namespace (DiffBind)
17: "croi_count_reads" not resolved from current namespace (DiffBind)
18: "c…
updated 7.0 years ago • tgjohnst
I'm now running ATAC-seq differential analysis by DiffBind with peaks from MACS2. I have 10 samples from batch 3 and 20 samples from batch 5. How could I eliminate batch effect...and normalize them in DiffBind? Sorry, I'm quite new in this area. Thanks!
Simon
span style="line-height:1.6">I am trying to reproduce the results of DiffBind for edgeR analysis.</span>
A member of my research group did analysis with DiffBind and got nice results, whereas me...performing the edgeR separately could not get any results.
DiffBind was called as follows:
<pre>
WNN_vs_WEN= dba.analyze(WNN_vs_WEN)
</pre>
According to DiffBind protocol: …
Hi there,
I am trying to use diffBind to obtain a set of consensus peaks and fold changes for three different transcription factors chipped. I am comparing...I only have one replicate as the second replicate has failed. As a result, I am getting errors from diffBind. Any advice on how to proceed? Thank you
I noticed a new vignette posted for DiffBind, which now includes an awesome option to plot data as a volcano plot. I would love to use this, but I cant seem to...I noticed a new vignette posted for DiffBind, which now includes an awesome option to plot data as a volcano plot. I would love to use this, but I cant seem to access this option in DiffBind even when updating the pac…
updated 7.6 years ago • andrew.gehrke
I'm now using DiffBind R package to conduct differential analysis for ATAC-seq dataset.
In this analysis, I want to compare each cell...I'm now using DiffBind R package to conduct differential analysis for ATAC-seq dataset.
In this analysis, I want to compare each cell type in two conditions, so I divided the general sheet into enclosed sheets with different cell names a…
running Diffbind, I don't find any significant differential binding sites. However, if I take the intersection of replicates in each...the other.
Those peaks should be statistically significant, but I am not sure I understand why DiffBind did not find any regions that are significant although some regions exist in one group but not the other after taking...the intersection of replicates in eac…
updated 21 months ago • narzouni
div class="preformatted">Hi Robin-
The HOMER peak format is not supported natively by DiffBind. You'll
need to convert the peak file format to a supported one -- the easiest
is the default ("raw") which has four columns...robinmjelle@gmail.com]
Sent: 29 March 2013 11:04
To: Rory Stark; gordon@cshl.edu
Subject: Fwd: diffbind
I addition to the previous mail I have this info:
> tcf7dat…
Hi,
I have been using DiffBind to perform differential binding analysis on ChIP-seq data, comparing two groups with 3 replicates for each. I am...Hi,
I have been using DiffBind to perform differential binding analysis on ChIP-seq data, comparing two groups with 3 replicates for each. I am now...any error message. In addition, this error message did not appear, when I use…
updated 8.4 years ago • shohei.hori
I am new to DiffBind. I have tried working with your test data and I have seen the tutorial online.
I am facing some issues with DiffBind...getting any peaks using DEseq2 and EdgeR in my data.
3. Can we compare 4 different conditions in DiffBind? Is there an example available with you with more than 'Resistance' and 'Restrained' conditions?
4. For MACS2, do we need...to provide specificall…
updated 2.7 years ago • Amandeep
div class="preformatted">Hi Igor-
We avoided adding annotation to DiffBind because of the other packages
that specialize in this. They don't take a DiffBind object directly,
but
you can always...Igor" <igor.dolgalev at="" nyumc.org="">
wrote:
>Hello.
>
>I am getting started with DiffBind. I am really enjoying all the
options
>it provides. Unfortunately, it d…
updated 10.2 years ago • Rory Stark
Hello,
I am interested in using diffbind to perform differential expression analysis on some ATAC data. However, all I have is counts table for peaks (no beds...Hello,
I am interested in using diffbind to perform differential expression analysis on some ATAC data. However, all I have is counts table for peaks (no beds or bams) and a meta table with the sample names and conditions they…
updated 5.7 years ago • pgontarz
<div class="preformatted">Hello Igor-
This feature has just been added to the upcoming release of DiffBind.
It
is part of Bioconductor 2.14, due to be released 14 April, and
currently
available in the Development branch.
dba.plotPCA has been reworked to use xyplot() from the lattice
package. It
now automatically draws a legend alongside the plot, and there is a
new
parameter, labels, for …
<div class="preformatted">Hi Anna-
I've shared the Dropbox location containing all the reads for the
vignette with you.
I do want to ask what version of DiffBind you are using (perhaps send
a sessionInfo() output?). The latest version (Bioconductor
2.13/DiffBind 1.8) has substantially new code for dba.count (using
much less memory) - you may want to check this out. Also, if memory
is an …
however, I need help at this point. My goal is to use pre-normalised data (e.g. using MAnorm) as DiffBind input so that later I can create contrast list (dba.contrast), reports (dba.report) and plot (dba.plotXYZ).
Question...output (MAnorm\_result\_commonPeak\_merged.xls) obtained after MAnorm normalization as an input for DiffBind?
Any help or recommendation is appreciated.
…
updated 4.0 years ago • ajeet
Hi all,
I am new to Diffbind and following the workflow from the handbook: https://bioconductor.org/packages/devel/bioc/vignettes/DiffBind...samples have 0 counts for all genes. check the counting script.
what is it that went wrong ?
my Diffbind version is (DiffBind_3.4.11)
Thanks
I have a couple questions regarding the dba.plotPCA function in diffbind. The relevant figures are here: <https://www.dropbox.com/sh/co3oywz8r745m8o/AACouCCG1q9UEyASR5igqXX9a?dl...I have a couple questions regarding the dba.plotPCA function in diffbind. The relevant figures are here: <https://www.dropbox.com/sh/co3oywz8r745m8o/AACouCCG1q9UEyASR5igqXX9a?dl=0>
I've been …
I am trying to compare two different conditions (with 2 replicates each) using Diffbind. For my Diffbind output, I'm getting 0 counts for one of the conditions and high counts for the other condition. This...to match my normalized browser tracks. There's clearly a peak around the chromosome position, but Diffbind is calculating it as 0 counts. There's definitely still a change in peak intensity b…
updated 22 months ago • slrpatty
Hi I am using Diffbind to report the DBS (I know that SICER has already a tool for doing so, but I have a huge dataset with different treatments...and I just want to try with DiffBind)
In any case, have you ever tried it? Even if the results that I get are good and consistent with other peak callers, it
style="line-height:1.6">heat map</span><span style="line-height:1.6"> plot which generation by diffBind.</span>
<span style="line-height:1.6">When we employing diffBind on those commands, it will generate </span>heat map
updated 9.6 years ago • yijing.su
I'm trying to use DiffBind for re-analyses of some data. The only files that are changed from my previous run of DiffBind are the peak files from...MACS2. They are still in the same format as before. Previously I was able to run Diffbind and analyse this same dataset without errors. However, now when I try the very first step of DiffBind (ta <- dba(sampleSheet
updated 9.4 years ago • mm2489
Hi,
I am new to diffbind and have a question about the GRange report generated from dba.report() function.
in the demonstrated report (tamoxifen.DB
updated 2.4 years ago • jonathanho1989
Hi community!
I am subsampling input control data for DiffBind analysis to test something. I have merged first input files by using samtools merge and then later samtools view...s "percentage of subsampling"
When I am trying to run DiffBind, then I get this error:
'subsampled\_input.bam' does not appear to be a BAM file (bad magic number)
Any ideas? I am browsing...in in…
Hi, Dr Stark.
In the [Question: diffBind: differentially bound sites are highly different between using EDGER and DESEQ2](https://support.bioconductor.org...full library size, total number of reads in BAM/SAM/BED file, instead of the peak count)** in Diffbind project.
Best wishes
Guandong Shang
updated 4.0 years ago • shangguandong1996
over input at that timepoint but is significant in the DiffBind? I know DiffBind and MACS2 are different methodologies. How does DiffBind take into account the input?
2. Due to the...consensus set I have the exact same number and location of peaks in the DiffBind output for B vs A and C vs A. I understand why this is the case. If I want to look at the differences in the peaks that are...the ti…
Hi,
I'm trying to understand what exactly is done by the dba.plotPCA function from DiffBind. I tried to reconstruct the plot generated by dba.plotPCA but for some reason I get a different plot. Could you...by the dba.plotPCA function?
Thanks!
Razvan
Here is what I've tried (I used DiffBind\_1.14.6):
library(DiffBind)
data(tamoxifen\_peaks)
dba.plo…
updated 8.9 years ago • r.chereji
After reading the vignette (https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf) I still have doubts on how grey lists are derived in `DiffBind` ? Could someone please explain
updated 3.4 years ago • Alexandre
Hi,
In the current version of DiffBind what are the steps for indicating that PE data is being used? Thank you.
Rob
 
updated 4.0 years ago • rbronste
I am hoping to get a little more information about how to use DiffBind to deal with spike-in recalibration and the vignette is a little sparse on this topic. In section 7.6 there's the following...I am hoping to get a little more information about how to use DiffBind to deal with spike-in recalibration and the vignette is a little sparse on this topic. In section 7.6 there's the following code:
…
updated 3.7 years ago • joselynn_wallace
I am using Diffbind to compare H3K27ac peaks between two time points. Recently, we added 4 more time points to the existing 2 to do time...series comparison.
From my understanding, Diffbind could conventionally compare and provide differential bound sites between 2 samples .
Q1: Is there a way to compare
Hi,
I ran diffbind and used edgeR and DESeq2.
I have a question regarding the normalized counts. In the DESeq2 analysis, the normalized...I actually get the opposite.
Can you help with this please?
Also, in the publication of the diffbind EdgeR was the default. Now DESeq2 is the default.
Do you have any preference to one of the methods?
Thanks a lot.
 
updated 8.4 years ago • GFM
preformatted">Hi Kasper-
>From 1.6 on, if the bLowMem parameter is set to TRUE in dba.count,
DiffBind will use summarizeOverlaps. Changing the config value
DBA$config$singleEnd to FALSE allows it to use paired-end...handles paired-end data.
Gord, how does the default count code handle paired-end data (in
pre-1.6 DiffBind, or when bLowMem=FALSE)?
Cheers-
Rory
________________________…
updated 11.4 years ago • Rory Stark
Currently I am using DiffBind for a project of my Bioinformatics study in Leiden, The Netherlands.
I am trying to run the followings commands in...steps of the manual:
(<a href="https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf" target="_blank">https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc...DiffBind.pd…
updated 7.0 years ago • bobfukkink
gt;
Cc: Daniele Merico
<daniele.merico@sickkids.ca<mailto:daniele.merico@sickkids.ca>>
Subject: Diffbind : use of controlBam
Dear Rory Stark ,
we used DiffBind with MACS peaks.
In our experiment, we had 3 biological replicates...control and tumor
replicate. This is approved by the MACS protocol.
When we load the MACS peaks in DiffBind, we are not sure if we can use
the same re…
Dear Bioconductor community,
I am interested in using DiffBind. I am following the procedure in "DiffBind: Differential binding analysis of ChIP-Seq peak data" and I got a bit confused...Dear Bioconductor community,
I am interested in using DiffBind. I am following the procedure in "DiffBind: Differential binding analysis of ChIP-Seq peak data" and I got a bit confused, I hope you can help me.&…
updated 8.0 years ago • omiguele
could you point it out to me so I can fix it?
3. In the case of plotting peaks (without counts), DiffBind first
merges all the overlapping peaks to form a master peak list. To
construct the vector for each peakset, it assigns...e.g. a
promoter), you may want to take a look at the MMDiff package -- you
can use your existing DiffBind objects in MMDiff.
4. Currently DiffBind will merge together an…
I've got a chip-seq dataset which I would like to analyse using DiffBind. I've tried Diffbind with one blocking factor and it works fine, but I was wondering how can I do it for three factors
I'm having trouble getting DiffBind v3.0.3 to work when installing through Conda from [here][1] - it fails with the error
> Error: package or namespace load...failed for ‘DiffBind’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace ‘dplyr’ 1.0.2 is being loaded, but >= 1.0.3...is required
Is it possible that the dplyr dependency…
Hi all,
I am running diffbind using narrowPeaks output from macs2
When using dba.count, I am taking each summit and counting reads +/-250 from the...summit so I'm expecting to see in the diffbind report that the width column only contains "501"
bindingmatrix <- dba.count(dbaobject, summits=250) \# summit +/- 250 bases
my scripts for differential ATAC-seq Binding Analysis and wanted to install an updated version of "DiffBind" Bioconductor package, in particular version 3.2.6 or 3.2.4 in whcih a specific little bug that was present in version...cannotnot find those updated versions (3.2.4 or 3.2.6)
https://anaconda.org/bioconda/bioconductor-diffbind/files
is there a way to use updated versions from anacond…
Hi,
I used DiffBind to count the ChIP-seq reads (dba.count) and plot the correlation heat map (dba.plotHeatmap), and a have a question. By...heat map and see which samples behave similarly. Could you please tell me if this is possible using DiffBind?
Thank you,
Razvan
updated 8.9 years ago • r.chereji
the consensus peak set extracted from diffbind is the counts of peak. if using the DESEQ method, diffbind will make analysis. so, can I directly use Deseq2 to analyze
Hi,</p>
<p style="direction: ltr;">I'm trying to analyze chip-seq histone modification data with diffBind. When I try running diffBind, it tells me that my bam files cannot be accessed. It was able to make the plot based on the
Hi all,
In using DiffBind I wanted to basically get a set on shared/diff peaks and wondering how to parse shared as being within a certain fold
updated 7.8 years ago • rbronste
Hello,
I am trying to convert fold values obtained from Diffbind table back to expression values (basically unlog it). My question is whether the log used to calculate the log fold...change is log or log2? I looked at the DiffBind manual and it says "The Fold column shows the log fold changes(LFCs) between the two groups, as calculated by the DESeq2
updated 18 months ago • bhandary.8590
We have basically three questions that revolve around the DESeq2 lfcShrink function which is used by DiffBind.
1. We have Cut&Tag samples and want to conduct differential binding analysis. Our main objective is to compare...two samples and see if there are any major peaks that are different. Do you think DiffBind is suitable to conduct such an analysis?
2. In the lfcShrink function th…
updated 17 months ago • bhandary.8590
Hi all (and hopefully Rory would see this. Thanks for the great program)
I have ChIP-seq data of 3 replicates of wild type and 3 replicates of my mutant.
I'm looking for loci where my protein binds in WT samples (so WT has peaks in the loci) but the mutant has no peaks (the protein doesn't bind to the same loci in the mutants).
I think this is what DiffBind manual explained as Occupan…
updated 2.1 years ago • Junsik
Hi Dr. Stark,
I was wondering if I could ask for your assistance with something DiffBind related please? My ChIP-seq experiment consists of five treatment groups (negative control, drug 1, drug 2, drug 3, drug...I do not have access to a high-performance computing cluster so am using the latest version of DiffBind in Galaxy for my analysis. For some reason the Galaxy version of DiffBind (2.10.…
updated 19 months ago • epipally
div class="preformatted">Hello Julian-
You should be able to install DiffBind on your linux using the
standard Bioconductor installation procedure (see
http://www.bioconductor.org/install...gt; biocLite("DiffBind")
This will figure out all the dependancies (there are a fair number),
and re-compile everything that needs compiling...Yuliy [rozenberg@med.unc.edu]
Sent: 03 May 2013 21:59
To: Ror…
gt; setwd("C:/Documents and Settings/pkunderfranco/Documenti/Data/ChIP-
seq Roberto/Analisi_PK/DiffBind/H3K27me3/")
> library("DiffBind")
> test= dba(sampleSheet='database.csv')
ES_H3K27 ES H3K27 1 1 raw
CMN_H3K27 CMN H3K27...Offset: 00003be1
Did anyone faced the same problem? which are the memory requirements
to run DiffBind?
Thanks,
Paolo
</div
Hi
I am using diffbind to identify perform DBA in ChIPRX normalized ChIP-seq data (https://doi.org/10.1016/j.celrep.2014.10.018). Since...I would like to use these trackfiles in place of the bamfiles for DBA. Is it possible to do this in Diffbind?
best
Ram
updated 5.7 years ago • ram.n.krishnan
Hi All,
I'm analyzing ATAC-seq data and use `` MACS2 `` for peak calling and `` DiffBind `` for occupancy and affinity analysis.
In occupancy analysis when I try to find peaks that are unique to one group...Hi All,
I'm analyzing ATAC-seq data and use `` MACS2 `` for peak calling and `` DiffBind `` for occupancy and affinity analysis.
In occupancy analysis when I try to find peaks that are uni…
Hello,
I am very new with DiffBind, so pardon me if it is a silly question.
I am trying to compare our ChIP-seq data with a published data set (GEO GSE322222...and they only provided BED files. I am wondering if it is possible to use DiffBind when we don't have access to BAM files (read and control).
Thanks,
Hosna
updated 7.2 years ago • jabbari
Wed, 28 Aug 2013 16:46:38 -0400
To: Rory Stark <rory.stark at="" cruk.cam.ac.uk="">
Subject: Re: DiffBind questions
Hi Dr. Stark,
I've been using DiffBind for my analysis and I have a question about
the
occupancy analysis...are two ways to use less memory in dba.count. The best way is
to
update to the latest version of DiffBind in Bioconductor 2.12.
dba.count
now has a parameter to do t…
updated 11.2 years ago • Rory Stark
about the interpretation of the colours assigned to the dots in the MA plots obtained with the DiffBind package:
red dots represent significantly differentially bound sites but what about the dark blue dots, the ones
Recent ...
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