Bioconductor Forum

As part of the latest Bioconductor release 3.12, `DiffBind 3.0` includes extensive updates of which users should be aware. The purpose of these updates, reflecting user comments...incorporating up-to-date methods and utilizing knowledge and experience gained in the 10 years since `DiffBind` was first written. The main updates are in the areas of **modelling**, **analysis**, **normalization**, …

Normalization ATACSeq ChIPSeq DiffBind chipseq

updated 3.9 years ago • Rory Stark

<div class="preformatted">Hi, Your sample sheet shows the same filename for "Reads" and "Peaks", which is unlikely to be right. The "Peaks" file should be the output of the peak caller (the peaks that MACS called); the "Reads" file should be the aligned reads, i.e. the *input* to the peak caller (the output of the alignment stage). Let me know if that fixes the problem. It should give a…

DiffBind DiffBind

updated 12.0 years ago • Gord Brown

Is it possible to run diffbind with my "own" binding affinity table? I might want to delete certain peaks or have my own way of combining peaks across

diffbind R

updated 4.3 years ago • maartenvandersande

Hi! I was wondering if there is a way to provide DiffBind with previously defined sizeFactors? I am using a calibrated ChIP-seq approach and can calculate normalisation

diffbind normalization

updated 4.1 years ago • nfursova.msu

<div class="preformatted">Hi Walter - You did the right thing by explicitly calling dba.contrast to add the WT vs KO contrast as there are only two knockouts. However you have two different factors (trimethyl and monomethly, I assume these are histone marks) for each condition. The warning from dba.analyze is that there were no differentially bound sites identified (with an FDR < …

Cancer edgeR DiffBind Cancer edgeR DiffBind

updated 11.8 years ago • Rory Stark

at="" perp.fr="" univ-=""> wrote: >Dear Rory, > >thank you very much for your DiffBind software. It s actually the only >software that allows us to identify differentially modified regions in >ChIPseq...is one mayor obstacle. As you will know, galaxy files have the >uniform .dat suffixe. However for DiffBind bamReads and bamControl file >format…

DiffBind DiffBind

updated 11.2 years ago • Rory Stark

Hi, I am finding the differential peaks using DiffBind, but my sample has no replicates. And my `SampleSheet` is ``` > dbObj <- dba(sampleSheet="SampleSheet.csv") trisomy_21...Hi, I am finding the differential peaks using DiffBind, but my sample has no replicates. And my `SampleSheet` is ``` > dbObj <- dba(sampleSheet="SampleSheet.csv") trisomy_21 fibroblas…

DiffBind

updated 5.1 years ago • zhangdengwei

Hi, Dr Stark. I want to do some interactions work when analysising ChIP-Seq or ATAC-Seq. So I decide to use the DiffBind count data as the DESeq2 input, and then use DESeq2 to get more complex design and to calculate FoldChange and pvalue. It seems I can perfectly repeat the log2FoldChange and paritially repeat pvalue. I have known some issues about DiffBind using DESeq2, and I am wondering w…

diffbind

updated 4.1 years ago • shangguandong1996

I am using DiffBind to determine differentially bound sites. When you extract the sites with dba.report, the GRanges object contains

diffbind granges

updated 10.0 years ago • igor

Hello, Thanks for your effort in producing such a good tool for analysis. Recently, I am using Diffbind to characterize differential open chromosome regions with ATAC-seq. I have more than 50 samples, equipping with...Hello, Thanks for your effort in producing such a good tool for analysis. Recently, I am using Diffbind to characterize differential open chromosome regions with ATAC-seq. …

DiffBind

updated 2.1 years ago • littlefishes20

Hello, I have successfully ran DiffBind on K4me3 and K9me3, so thanks for the very clear Vignette! However, I probably missed a key information : I am wondering...if the peaks I'm feeding DiffBind should be FDR filtered or not. I called peaks using MACS3 which has a default FDR filtering <0.05 and obtained between...is : should I call peaks with MACS3 without the default FDR filtering, …

ChIPSeq DiffBind

updated 2.7 years ago • rita.rebollo

Hi Rory, I was trying to plot, using DiffBind\_2.2.12, a Venn diagram for the following contrast (the only one present in my DBA object): <pre> 1 Contrast: Group1 Members1

diffbind

updated 7.5 years ago • Silvia

div class="preformatted">Hi I have been trying to use DiffBind to analyze our Chip-seq data and have been running into some errors repeatedly. I first created a samplesheet.csv...each and the peaks were called using MACS v2. The peak caller generated .bed files which was used in DiffBind. I defined the working directory in R first. I then read the sample sheet in : > H3K4.B73=dba(s…

DiffBind DiffBind

updated 11.2 years ago • Anitha Sundararajan

This is a question on the dba.report function in DiffBind. I am trying to retrieve all sites (including non-differential and differential sites) by using the following script...the dba.report function to retrieve all the sites. I would appreciate any suggestions on this. My DiffBind version is 1.12.0 Thanks, Mei San

diffbind

updated 9.6 years ago • meisan406

Hi! I'm using DiffBind for ATAC-seq data, and everything runs smoothly except one thing -> I cant make a dba.report for one of my contrasts

diffbind

updated 7.6 years ago • j.bergenstrahle

Hi, I'm currently using Diffbind for my ATAC-seq pipeline. After calling the dba.analyze function you can do various plots via e.g. dba.plotMA

diffbind

updated 7.6 years ago • j.bergenstrahle

For `DiffBind` users, there is a new function in **Bioconductor 3.13**, `dba.plotProfile()`, that makes it straightforward to calculate...For `DiffBind` users, there is a new function in **Bioconductor 3.13**, `dba.plotProfile()`, that makes it straightforward to calculate peak profiles and generate complex heatmap plots. `dba.plotProfile()` flexibly packages different sets of sites and sample…

profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq

updated 3.5 years ago • Rory Stark

Hello Rory, I am using diffbind to extract the raw counts for my PEAKS. I used the function myData.RawCount <- dba.count(myData, score=DBA\_SCORE

diffbind

updated 8.6 years ago • galib36

green when it comes to understanding the intricacies of R packages. I have read through the DiffBind package vignette a few times, and have tried going through the source code to help me, but I am still trying to understand...the meaning of some of the plots that come out of the DiffBind package, namely `plotHeatmap()` and `dba.plotPCA()`. I can run through a pipeline of the package without issue…

DiffBind PCA Differential Analysis

updated 4.7 years ago • jrp208

to figure out what is being returned. After you call dba: > setwd(system.file("extra", package="DiffBind")) > tamoxifen=dba(sampleSheet="tamoxifen.csv",peakFormat="bed") Try seeing what "tamoxifen" has been set to: > tamoxifen...mailto:rory.stark@cruk.cam.ac.uk>> Subject: RE: data process before overlap analysis with the DiffBind Thanks a lot. At 2014-03-11 23:12:…

PROcess DiffBind PROcess DiffBind

updated 10.7 years ago • Rory Stark

1) Doubt about DiffBind's MA plots in general** Hello, I am doing ChIP-seq analysis of H3K4me3 in human samples across different conditions...For that, my pipeline includes DiffBind to make volcano, MA plots , PCA and heatmaps. The DiffBind manual says that MA plots are good to see the effect of normalization...this image in the manual I don't think it's symmetrical. Therefore, I was wondering t…

diffbind R MAplot Chipseq

updated 5.5 years ago • melnuesch

Hi all, I'm new to ATAC-seq analysis and have recently been trying to use DiffBind to systematically identify differential peaks that I've been seeing by eye when looking at macs2 output in IGV...Hi all, I'm new to ATAC-seq analysis and have recently been trying to use DiffBind to systematically identify differential peaks that I've been seeing by eye when looking at macs2 output in IGV. …

DiffBind ATACSeq

updated 16 months ago • Nebat

Hi Dr. Rory Stark,         I used your "DiffBind" to analysis Chip-seq data by following codes. However, I could not get the table which used to plot heatmap (different...setwd("/data/fmao/rajesh/hMeDIP/DiffBind") pdf("draw.DiffBind.final.pdf") hmedip <- dba(sampleSheet="config.csv")     plot(hmedip,main="using occupancy

annotation

updated 8.0 years ago • maofengbiao

Seq analysis hence this may be a basic question. I want to do differential binding analysis using DiffBind on H3K4me3 and HeK4Ac histone peaks called using macs2 in two different conditions. I am following the tutorial...ChiP-Seq. Could someone please suggest me what to use for summits size for histone ChiP-Seq for DiffBind? Thanks so much!! &nbsp

Diffbind Histone Chip-Seq Summit size

updated 7.2 years ago • urjaswita

Happy new year folks !!! I used the Diffbind vignette and ran the commands provided in Rstudio. However, the Intervals in the dba object do not match with the...vignette. It would be great if you could help me out with this. Thanks in advance. ``` dba object in Diffbind vignette > tamoxifen 11 Samples, 2845 sites in matrix (3795 total): ID Tissue Factor Condition Treatment Replicate...…

DiffBind

updated 2.9 years ago • Ayyappa

Happy new year folks !!! I used the Diffbind vignette and ran the commands provided in Rstudio. However, the Intervals in the dba object do not match with the...It would be great if you could help me out with this. Thanks in advance. ``` dba object in Diffbind vignette > tamoxifen 11 Samples, 2845 sites in matrix (3795 total): ID Tissue Factor Condition Treatment Replicate...…

DiffBind

updated 2.9 years ago • Ayyappa

Hi all, I using DiffBind to compare WT vs Treatment ATAC-seq samples and I have two questions/problems regarding the DiffBind `` dba.report...Treat_1.bed Treat_2,hs,ATAC,Treat,2,Treat_2.bam,,Treat_2.bed</pre> Code: <pre> ## Load DiffBind sample design. ATAC.dba = dba(sampleSheet = "csv/samples.csv", peakFormat = "bed") ## Count reads in binding site intervals

diffbind differential binding analysis R report

updated 6.9 years ago • hlsz.laszlo

Hello, @rory I have a question regarding the 3 scenarios in which lfcShrink is applied in DiffBind package. The source code looks like this ``` if(shrink) { if(contrast$contrastType=="byname") { res$de <- suppressMessages...Hello, @rory I have a question regarding the 3 scenarios in which lfcShrink is applied in DiffBind package. The source code looks like this ``` …

FoldChange DiffBind lfcShrink

updated 16 months ago • bhandary.8590

Hi there! I am currently using DiffBind v3.2.7 to analyse some ChIP-seq data for RNA Polymerase III (RNAPIII). We have Drosophila spike-in chromatin in the...samples that I would like to use in DiffBind to normalise the data. The problem is that during library prep, some of the samples accidentally got different proportions...in chromatin relative to sample chromatin. My question is wheth…

DiffBind ChIPSeq Normalization SpikeIn

updated 3.2 years ago • Drew

Hi, The descriptions of score methods in DiffBind manual are trimmed and cannot be understood in its pdf file (fig1). Could you provide them for me to learn? Many thanks

DiffBind dba.count score manual PDF

updated 8.0 years ago • Gary

I have been trying to change font sizes for my box plots in DiffBind: <pre> dba.plotBox(x, th = 0.05, pars = list(cex.axis=1.5, cex.main=2, cex.lab=1.5))</pre> I have also tried the following variation...dba.plotBox()</code><span style="white-space:pre-wrap">? I would prefer to be able to do this in Diffbind without having to re-draw the plot directly with boxplot().<…

diffbind

updated 6.5 years ago • Mthabisi Moyo

Hi, I am trying to understand PCA plot I generated using Diffbind. I used this code ss <- read.csv("samplesheet.csv") obj <- dba(sampleSheet=ss, scoreCol=5, minOverlap=1) # get counts (mapQCth...DESeq2 and plotting PCA on both vst transformed counts and raw counts. The PCA obtained from diffbind looks more similar to raw counts than vst. So what I am doing wr…

DiffBind PCAplot

updated 8 months ago • Ankit

whole list of samples on the plot, how can I increase the width of the correlation plot generated by DiffBind

DiffBind plot(DBdata)

updated 5.3 years ago • researcher

Hi I am using diffbind package to analyze my Chip seq data. I have bed files in my hand. I have arranged my input sample sheet (PFA). I am getting...this error. Could you please help me to solve this issue? > library(DiffBind) > Data <- dba(sampleSheet="SampleInfonew.txt") 1 NA raw Error in if (is.na(peaks)) { : argument is of length zero Reg…

DiffBind ChIPchip

updated 3.9 years ago • shrinka.genetics

Hello, I am using DiffBind and coming across an error using code that worked just fine a few months ago. I now can't seem to make a dba object. I am

DiffBind dba R error

updated 5.3 years ago • annika-helverson

DiffBind is very simple, see below, and worked flawlessly so far. We however recently updated our Singularity image, and we now...work with a newer DiffBind package version. Unfortunately, the new(er) versions either introduce a new bug (see below) or at least an undocumented...results in 0 consensus peak sets. I have reproducible code that runs just fine when running with DIffBind 2.14, but resu…

DiffBind

updated 2.5 years ago • chrarnold

22:31 +0000 To: Rory Stark <rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>> Subject: DiffBind loading Problem Dear Rory and Gordon, I would like to use DiffBind to compare my ChIPseq data in which I have two different

Transcription ChIPSeq chipseq DiffBind Transcription ChIPSeq chipseq DiffBind

updated 10.8 years ago • Rory Stark

errors upon running `` ChIPQCreport ``. These various errors were all resolved, once I upgraded DiffBind to the latest version (2.4.4). ChIPQC should therefore install the latest available version or try to upgrade any

chipqc diffbind chipqcreport

updated 7.5 years ago • Coby Viner

Hi, I have been using diffbind for a while now, and I use this code to generate a results file: <pre> d_all.DB <- dba.report(d_all, contrast=1, method...Hi, I have been using diffbind for a while now, and I use this code to generate a results file: <pre> d_all.DB <- dba.report(d_all, contrast=1, method=DBA_DESEQ2

diffbind dba.report

updated 7.4 years ago • wesley.cai

<div class="preformatted">Dear All, I am trying to use DiffBind and having an error. The data set is just two conditions without any replicates. I set up the contrast manually as groups...div class="preformatted">Dear All, I am trying to use DiffBind and having an error. The data set is just two conditions without any replicates. I set up the contrast manually as

DiffBind DiffBind

updated 11.0 years ago • Kasthuri Kannan

p/255052/  [Devon Ryan](https://www.biostars.org/u/7403/)  kindly suggested to use DiffBind to "normalize only to non-peak regions", I checked "DiffBind", could not find the options he referred to. But maybe I missed...some key points. So if "Diffbind" could help solve my issue, please kindly let me know.  &nbsp

deseq2 diffbind

updated 7.5 years ago • JunLVI

Hi, I'm using DiffBind to analyze a set of ChIP sequencing data. For each sample, I have three biological replicates. I performed the ChIP

fold enrichment values using DiffBind

updated 9.9 years ago • robertacar

on whether it is considered in differential binding analysis. Also, nothing is mentioned in the Diffbind vignette. Could you please explain how this strategy might affect using the diffbind package? I greatly appreciate

diffbind chipseq chipqc

updated 4.1 years ago • bioinfouser2

Hi I am using DiffBind for analyses of my Chip-seq results. I was wondering if there is any way I can get the original peak fold enrichment...scores (from MACS2 output) for the consensus peak set that DiffBind generates.   Thanks   &nbsp

diffbind

updated 9.6 years ago • mm2489

<div class="preformatted">Hi again, I am trying DiffBind and loaded my data that looks like this: H3K4m3 4 Samples, 13203 sites in matrix (13792 total): ID Tissue Factor Condition Peak.caller Replicate Intervals 1 wt1 Hela H3K4me3 control1 raw 1 14111 2 wt2 Hela H3K4me3 control2 raw 2 13771 3 treat1 Hela H3K4me3 condition1 …

Genetics DiffBind Genetics DiffBind

updated 12.2 years ago • António Miguel de Jesus Domingues

div class="preformatted">Dear list, I made a new samplesheet to use with DiffBind with this format: SampleID Tissue Factor Condition Replicate bamReads bamControl Peaks Contrl1 Neural K9 Resistant...more categories, or lower value for minMembers. ->My questions are: -What is the contrast for DiffBind (I added the input for each set of samples, and 2 b…

Alignment DiffBind Alignment DiffBind

updated 11.8 years ago • José Luis Lavín

Hello, I'm using DiffBind to extract peaks that appear in my replicates. I have four replicates, and I wish to fetch peaks that are in at least

DiffBind

updated 2.8 years ago • Krista

student trying to analyse Chip-seq data generated in my project but I'm loosing it to use properly DiffBind package even if I read several times the manual. To illustrate my work : Chip-seq on flies: * 3 Lineages (A, B and C) x 3 treatments...nbsp;   In treatment CO, difference between A and B , B and C... If I understand the Diffbind package usage : 1. I imported data …

diffbind chip-seq R

updated 6.2 years ago • pierre.marin

Hello everyone, I would like to have some help to a retrieve a matrix or add additional features to the DiffBind heatmap. So fare, I am using the DiffBind R package and I would like to show the correlation factors in the heatmap as numbers in the different tiles or as an alternative save the matrix, which is used to generate the heatmap to take the correlations factors from there. I am using…

DiffBind

updated 3.1 years ago • Katrin

that is generated is based on the scores that the BED files contain or are the scores calculated by Diffbind itself? What if the bed files do not have a score column (only chr \#, start, end, name is present)? How is the score calculated

diffbind heatmap pearsoncorrelation

updated 8.4 years ago • shubhibartaria

In DiffBind when you draw a heatmap based on an experiment with a small number of observations the labels are quite large and

diffbind labels heatmap

updated 7.0 years ago • epstein

Hi, I have peak file for four different condition without replicate. I converted the text file to Bed file by taking column 2,3,4,8 and 5 which is chr, start, end, score and strand respectively and also removed first 40 line having "\#' in the begining. and then created samplesheet "sample.csv" having column Id, tissue, condition, bamreads, bamconrtol, peak, peakcaller. steps I followed librar…

diffbind

updated 9.3 years ago • Gyan Prakash Mishra

Hi, I'm trying to use DiffBind for my ChIPseq analysis, but I encountered the following "problem". I loaded two patients' groups of samples using...Hi, I'm trying to use DiffBind for my ChIPseq analysis, but I encountered the following "problem". I loaded two patients' groups of samples using dba

DiffBind minOverlap consensus peakset Job

updated 5.1 years ago • mademoisElle

200bp-2kb and this corroborates what I see when I view the BAM files in IGV.</span> I then used DiffBind to look for peaks that are significantly different between my FLAG-tagged samples and those that lack the tag. This

diffbind

updated 9.5 years ago • dsherw

as I understand, one can use the argument minOverlap in dba.count to achieve that, but this forces DiffBind to count the reads again -- which takes a significant amount of time and IO bandwidth. Is there a way to obtain the counts

diffbind

updated 7.4 years ago • Roger

Dear all, I am analysing ChIP-Seq data and used DiffBind to compare 3 wildtype vs 3 mutant samples. When calling dba.report(myDBAObject, th=1, bUsePval=TRUE) I receive odd...Dear all, I am analysing ChIP-Seq data and used DiffBind to compare 3 wildtype vs 3 mutant samples. When calling dba.report(myDBAObject, th=1, bUsePval=TRUE) I receive odd FDR

diffbind

updated 8.3 years ago • biotom

the following columns: ......,log2Foldchange,lfcSE,pvalue,padj For the ChIP-Seq I have used diffbind to perform the deseq analysis, and extracted the deseq2 object using DBA.report and and now it has the following...to be evenly disributed over a range (-4 to -4), with alot of genes showing no major changes. The diffbind DESEQ2 analysis however yield a strange scatterplot pattern where ther…

DiffBind ChIPSeqData DESeq2

updated 7 months ago • marcusn

in my bam files) the chromosome names do not have "chr", and I guess that in the chromosome names DiffBind uses they do. Is it possible to circumvent it and what would it take? I can clean the blacklisted peaks by myself, using...bedtools; but when it comes to greylists, I would be glad to enjoy the automatic use of greylists in DiffBind. Is there any solution for it (perhaps using the difflo…

DiffBind

updated 3.7 years ago • Sam

Hello everyone, I’m working on a set of ChIP-Seq samples and I’ve started to use DiffBind to proceed to my differential analysis. My experimental design is the following : 2 conditions : Glucose (control...Hello everyone, I’m working on a set of ChIP-Seq samples and I’ve started to use DiffBind to proceed to my differential analysis. My experimental design is the following : 2 condition…

ChIPSeq DiffBind ExperimentalDesign

updated 3.7 years ago • SFn

When I set the contrast in DiffBind as ``` # Contrast from normalized object dbObj_contrast_manual <- dba.contrast(dbObj_norm, design="~Condition") dbObj_contrast_cells

DiffBind

updated 11 months ago • Sam