Bioconductor Forum

analyzing H3K27ac marks across multiple tissues. I have the following sample sheet (simplified) for DiffBind: | SampleID | Tissue | Factor | Condition | Replicate | |-------------------------|---------------|----------|---------------|-----------| | H3K27ac_adipose_r1 | adipose | H3K27ac | OtherTissues | r1 | | H3K27ac_adipose_r2...OtherTissue…

DiffBind

updated 7 months ago • lryrainche

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 18 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 4.6 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 4.6 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 22 months ago • Sam

Hello, I am analyzing some ChIP-seq data with Diffbind, and everything works great until when I was trying to use its plotprofile funtion. The command and error messages

ChIPSeq profileplyr DiffBind

updated 4.2 years ago • zhuyi05

I have a very simple question regarding the dba.plotProfile function in Diffbind. I couldn't find an answer online, but would appreciate someone linking the answer, if it already exists somewhere

DiffBind

updated 14 months ago • Tara

do not get any significant peaks by MACS, so the output peaks file is empty. When I use that file in DiffBind sample sheet, I get an error: <pre> Error in read.table(fn, blank.lines.skip = T, header = T) : no lines available in input Calls

diffbind chipseq

updated 9.3 years ago • igor

div class="preformatted">Dear Dr. Brown, I asked the questions earlier regarding the DiffBind last week. I have versioned up to R3.0.1 and Bioconductor 2.12, and I checked to see how DiffBind 1.6.2 works. But the...still crashes in the bed data and I attached the logs of the bed data below. Since the versioned up DiffBind 1.6.2 output the GEO DATA as an Alignment Data Sample, I downloaded t…

GO DiffBind GO DiffBind

updated 12.4 years ago • kentanaka@chiba-u.jp

Love the new design feature of DiffBind! However, I am having trouble writing the contrast for the interaction terms. I've used this [tutorial][1] for writing...contrasts in DESeq2 for RNA seq results and thought the approach would work in DiffBind. ```r DBA <- dba.contrast(DBA, design = '~ Condition * Treatment') DBA$DESeq2 $names [1] "Intercept" "Condition_MUT_vs_…

DiffBind

updated 4.6 years ago • lindsaynhayes

don't know whether the difference is due to real biology, or due to some technical problem. I used DiffBind for detecting differential H3K27Ac. As expected I get much more peaks which are up at the disease tissue. Are there...any suggestions for what would be the best normalization in DiffBind in such a case, or how can I try understanding whether this is an artifact? Thank you

DiffBind

updated 5.0 years ago • GFM

Hello, I tried to do test run of Diffbind for my ChIP-seq data. I followed the manual and used the basic command. these are my command :    library(DiffBind) setwd("/project/maheshid/mforoo1/DiffBind") samples <- read.csv("H3K4me3.csv", header=TRUE) names(samples) samples</span

rory stark

updated 8.4 years ago • mforoo1

Hi all, So am using the diffbind R package and I was doing some plots after analyzing my samples. using the dba.plotVolcano and the option > bLabels

diffbind

updated 6.2 years ago • theodore.georgomanolis

cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>> Subject: Have I extracted the right data with DiffBind? Dear Stark, I have 17 peaksets wiht four examples in the mail attachments. I want to extract ranges shared by at least...4 of the 17 peaksets. And then I run the following code under "DiffBind" package: >bedfilelist2=dba(sampleSheet="bedfilelist2.csv",attributes=DBA_ID,c…

updated 11.6 years ago • Rory Stark

Dear Rory   First I wan to thank you for making Diffbind an easy access tool. I have been using it a lot and I have a couple of questions.   I have been looking for a description

normalization chipseq diffbind

updated 10.8 years ago • medinaale

Hi, I'm having issue with dba.contrast() in DiffBind v3.4.0. I have two conditions, and each condition has 3 replicates. I'm working a simple differential peak analysis

v3.4.0 DiffBind

updated 3.9 years ago • AMA

are from different tissues, no replicate. I want to differentiate them according to 5 conditions by DiffBind package, and display result on heatmap. So I did as follows: >ALL <- dba(sampleSheet="mysamples.csv") >ALL\_count

diffbind

updated 7.2 years ago • mengm5

the problem and the peaksets are read in. The question is if the peak scores are considered by DiffBind at all, and if the problem that arises later on (no way to get beyond __factorname = dba.analyze(factorname) __is a result

diffbind

updated 10.5 years ago • iliya.lefterov

theresas@usc.edu] Sent: 15 February 2014 02:01 To: Rory Stark; Gordon Brown Subject: minOverlap in DiffBind in R- what does it mean? Greetings Drs, Stark and Brown, my name is Theresa. I have just started using DiffBind and can't...package. I have gone through your tamoxifen tutorial and have read through forums and threads on DiffBind online. but I still can't ferret out what "minOverlaps=…

DiffBind DiffBind

updated 11.7 years ago • Rory Stark

wherein I am given a few BED and BAM files to analyse and see how similar they are. I am using the diffbind package to do so. The first correlation map(heat map), when I run >>>MB <- dba(sampleSheet="MBdataframe.csv")&nbsp

diffbind heatmap

updated 9.3 years ago • shubhibartaria

Hello! I have a really basic question! In the `DiffBind` vignette, I have a question regarding the following texts: > If bFullLibrarySize is set to TRUE (default), then sizeFactors...sample, divided by the minimum of these; otherwise, estimateSizeFactors is invoked. How does `DiffBind` internally calculates the number of reads of a BAM file to make those *sizeFactors*? In par…

DiffBind ChIP-seq

updated 5.4 years ago • bioinfouser2

Hello everyone, I have a simple question; I am doing a DiffBind analysis and using dba.contrast function what's the difference if we do in diffBind contrast ie: WT vs Control and

DiffBind

updated 17 months ago • zzrammal

the body of text here Code should be placed in three backticks as shown below ```library(DiffBind) getwd() setwd("/Users/tsompana/Box/6. PROJECTS/8. Justin.Fasting.Enzalutamide.ATAC-seq/3.DiffBind/3.DiffBind_csv_files...csv file samples = read.csv("Screening.csv", header=TRUE, sep=",") #read peaksets using the "dba" DiffBind function screening = dba(sampleSheet = "Screening.csv") s…

bam bai DiffBind dba.count Diffbind

updated 4.2 years ago • mtsompana

Hi, DiffBind (v3.4.11) dba.analyze function doesn't have bSubControl option anymore? dba.analyze function (bGreylist=FALSE

DiffBind

updated 2.1 years ago • r.murakami

Hi, Using DESEQ2 and EDGER in diffBind gives huge difference in total number of differentially bound sites around 8000 for DESEQ2 and around 700 for...Hi, Using DESEQ2 and EDGER in diffBind gives huge difference in total number of differentially bound sites around 8000 for DESEQ2 and around 700 for EDGER

diffbind

updated 6.2 years ago • dewshrs

Hi all, I am trying to find which genes are different in chromatin accessibility so I used nf-core/ATAC pipeline then feed the bam files and broadpeak files output into Diffbind. I got around 100k peaks, 21k genes after annotated peaks by ChIPpeakanno, and after sorting the top genes by Fold. I...so I used nf-core/ATAC pipeline then feed the bam files and broadpeak files output into Diffbind. I g…

DiffBind

updated 2.4 years ago • Chris

When I used dba.cout with DiffBind， the following error occurred. Code should be placed in three backticks as shown below ```r library(DiffBind) library

DiffBind dba.count

updated 3.8 years ago • tjhwangxiong

nbsp;         I am trying to analyze ChIP-Seq data using DiffBind. After creating a CSV file with the experiment design and the peak files information. like shown in the DiffBind vignette...utils     datasets  methods \[8\] base other attached packages: \[1\] DiffBind\_1.8.5…

diffbind reading peaks

updated 10.6 years ago • surjray

Hi, I'm using DiffBind for many of my ChIPseq analyses and recently asked myself, if the "concentration" that is given as output of dba.report

DiffBind

updated 4.6 years ago • roman.hillje

Hi,  I got an error when I used DiffBind to treat a human ATAC-seq library data set. (see  https://support.bioconductor.org/p/94915/).ATAC-seq is the data...Hi,  I got an error when I used DiffBind to treat a human ATAC-seq library data set. (see  https://support.bioconductor.org/p/94915/).ATAC-seq is the data set

atac-seq diffbind

updated 8.5 years ago • zhaolin20042008

I would do this if A) is the right answer. However, if it is B) then IDR is somewhat redundant, as diffbind would just tell me all of the peaks that are significant.  Thanks in advance. -Wes

peakset diffbind

updated 8.9 years ago • wesley.cai

<div class="preformatted">Hi Marta- Well spotted! I have been able to reproduce the behavior you describe, and found the cause. edgeR tends to report normalized counts-per-million (cpm), which is good for comparing counts between experiments but uses values that are potentially on a much different scale than for the original experiment. Instead of scaling every experiment to one million r…

Transcription Normalization DiffBind Transcription Normalization DiffBind

updated 11.7 years ago • Rory Stark

My output files from the Genrich are .log and .narroPeak files. Can I use the peak files in DiffBind? Thanks! Gayani

DiffBind Genrich

updated 6.6 years ago • gsenevirathne

Hi! DiffBind is great stuff! I am trying to do a DiffBind analysis comparing 6 conditions (CT00, CT04, CT08, CT12, CT16, CT20). I have managed...output only reported Conc\_CT00 and Conc\_CT04. So, what do the 21 contrast mean? Should I do one DiffBind analysis for each pairwise comparison (CT00-CT04, CT00-CT08, CT00-CT12...CT16-CT20)? &nbsp

diffbind

updated 9.6 years ago • j.m.fustin27

Hi, I'm confused by how DiffBind uses the spike-ins for normalization. My understanding of the manual is that DiffBind calculates the spike-in reads

SpikeIn DiffBind

updated 2.6 years ago • Weisheng

normalised read counts should be used. You can work with RPKM values for the plotting features of DiffBind (by setting score=DBA_SCORE_PRKM in the plotting function, or in dba.count, where the score can be reset at will if...aur?lie teissandier" <aurelie.teissandier at="" curie.fr=""> wrote: >Dear Rory, > >I use diffbind with Deseq. And I look in the newCountDataSet ob…

DESeq DiffBind DESeq DiffBind

updated 11.8 years ago • Rory Stark

such that one can look at the plot and see the density along the length of the chromosome. From the diffbind table, what column can I use to plot the read density? Can I use the Fold column? Thank you so much for any help or guidance

Read density DiffBind

updated 2.6 years ago • bhandary.8590

Hi Everyone I have ChIP-Seq in a strain with defined maternal/paternal background and Now I want to use DiffBind to perform allele-specifc binding analysis. But what should be the design of analysis in this case? I can think of different...I have ChIP-Seq in a strain with defined maternal/paternal background and Now I want to use DiffBind to perform allele-specifc binding analysis. But what shou…

diffbind chipseq

updated 10.5 years ago • Vivek.b

I retrieve DiffBind results as a DESeq2 object, and then look how many differentially bound regions are within it. When doing this, I get...a different number of DB regions compared to the original DiffBind object. ```r library(DESeq2) library(DiffBind) data(tamoxifen_counts) tamoxifen <- dba.contrast(tamoxifen, design

DiffBind

updated 4.6 years ago • Sam

normalization was set to spike-in. I'm now planning to conduct differential analysis with DiffBind and have included the spike-in BAM files in my sample sheet. Could someone please advise on the appropriate parameters

Normalization DiffBind

updated 11 months ago • kim

div class="preformatted">Dear Rory, I finally analyze my data with DiffBind and it seems working well, I was wondering whether is possible or it will be possible in the next release to export

DiffBind DiffBind

updated 13.1 years ago • Paolo Kunderfranco

Hi, I am getting the following errors while using DiffBind to output the peakset . dba(data, bSummarizedExperiment=TRUE) Error in FUN(X\[\[i\]\], ...) :   assay rownames() must be NULL or equal

DiffBind

updated 9.1 years ago • svohra

differential peak finding, drawing Venn diagram and PCA plot) my m6A-seq data recently using DiffBind. However, as the program is developed originally for analyzing ChIP-seq data, I'm hesitant to apply default settings...events will make aligner generate large gaps between alignments. So maybe some parameters of DiffBind should also be tweaked manually. I'm wondering which parameter should I part…

DiffBind MeRIP-seq m6A-seq

updated 2.6 years ago • zhiyi

I am learning the DiffBind package, and I have some questions not covered by the vignette. 1) Is the peak score relevant to **affinity** analysis...I am learning the DiffBind package, and I have some questions not covered by the vignette. 1) Is the peak score relevant to **affinity** analysis, and

DiffBind

updated 4.6 years ago • Sam

each factor might have different frip, and it can cause biases in the comparisons. Is it OK to use DiffBind / csaw to compare these two ChIP seq samples (with replicates of course)? Thanks

DiffBind csaw

updated 5.4 years ago • GFM

I've been trying to use DiffBind for ATAC-seq data. I noticed that there is a large difference in differential accessibility depending on whether

diffbind atac

updated 6.7 years ago • paz2005

nbsp; I have questions about "dba.report", I applied "DiffBind" to analyze my dataset like:   <pre> H3K27ac_CellA_CellD <- dba(sampleSheet="sampleconfiguration.csv",) H3K27ac_CellA_CellD_Count

diffbind

updated 8.4 years ago • JunLVI

Hello, I am quite comfused about the mechanism and detailed process of background normalization in diffbind normalization. As the manual depicted, "The core background normalization technique is to divide the genome into

Normalization DiffBind

updated 12 months ago • Young Boqin

two things: the first is to override the column choice given above, so that I can for instance force DiffBind to use signalValue column; the second is to indicate normalization is TRUE/FALSE. Thank you Teck Por Lim National

DiffBind chipseq

updated 10.5 years ago • teckpor

Hi, I'm trying to understand the normalization for DESeq2 analysis within DiffBind.  If I run: <code>Pool1 = dba.analyze(Pool1,method=DBA_DESEQ2,bFullLibrarySize=FALSE,bCorPlot...Hi, I'm trying to understand the normalization for DESeq2 analysis within DiffBind.  If I run: <code>Pool1 = dba.analyze(Pool1,method=DBA_DESEQ2,<strong&g…

diffbind deseq2

updated 10.4 years ago • JasonLouisStein

Hello,  I am trying to use diffbind on paired end read data. I have done the following to get our proper peaks of interest ( we have technical replicates

diffbind

updated 10.0 years ago • jess.schust

Hi, We use DiffBind for the differential binding analysis of our ChIP data. In this we use edgeR TMM for normalization. I would like to...really appreciated. Thank you. ``` indiff <- dba(sampleSheet="//smb.cluster/080719ATACseq/Diffbind/SampleSheets/AAG57_0v2_SampleSheet_desktop.csv") indiff indiff_count <- dba.count(indiff, minOverlap=2) indiff_count...norm$lib.sizes/n…

edgeR Normalization DiffBind

updated 4.4 years ago • Nico

Dear all, I am using DiffBind for ChIP-Seq and CUTnTag analysis and would like to switch off subtracting reads of control samples. For this, I set...bSubControl=FALSE` in `dba.count()`. However, DiffBind results are exactly identical no matter if I set bSubControl to TRUE or FALSE. I tried this for several R and DiffBind

bSubControl ChIPSeq DiffBind

updated 21 months ago • frueher

But I don't want to get a consensus peak set. So I add "peaks=NULL" according to the document of DiffBind. Here is my code: ``` > data$config$singleEnd <- F > data <- dba.count(data,peaks=NULL,bUseSummarizeOverlaps=T) Error

software error

updated 6.0 years ago • shen_

Hello I am using DiffBind for ATAC-Seq analysis. I would like to remove peaks located on random chromosomes and chrUn (Unplace Chromosome...Hello I am using DiffBind for ATAC-Seq analysis. I would like to remove peaks located on random chromosomes and chrUn (Unplace Chromosome). I

DiffBind

updated 14 months ago • mdidish

0, 0)">ifferential binding analysis of ChIP-Seq peak data with DiffBind. I´m trying to use the code explained in the post: https://support.bioconductor.org...peaksets between TFa and TFb. Here I paste the output from the console:   > library(…

diffbind

updated 9.6 years ago • jvdelarosa

Hello, I'm new to DiffBind and have 3 tissues with 2 replicates each. I have been able to generate plots with contrast 1-3 to compare each pair

DiffBind

updated 4.9 years ago • Divya

I'm trying to prevent Diffbind from merging overlapping peaks in my bed file (TSS file with exactly 2000 bp widths) by setting DBA$config$mergeOverlap

DiffBind

updated 2.7 years ago • slrpatty

Hi everyone, im trying to install Diffbind to identify unique enriched peaks from treatment and control data. i cant able to install diffbind in R it shows error...status 28: In install.packages(pkgs = doing, lib = lib, ...) :   installation of package ‘DiffBind’ had non-zero exit status   &nbsp

DiffBind

updated 9.1 years ago • gskbioinfo143

I am a little puzzled by the way of generating a dba report from DiffBind matrix. When I run dba.report(mat, contrast=1), this should run with default fold and p-values, which should be 1 (fold...I am a little puzzled by the way of generating a dba report from DiffBind matrix. When I run dba.report(mat, contrast=1), this should run with default fold and p-values, which should be 1 (fold) and

DiffBind

updated 12 months ago • aelbassiouny