Bioconductor Forum

Hi! I am trying to run Diffbind for differential enrichment analysis of my ChIP-seq datasets. To start with, .broadPeak bed files (both ChIP & Input...and .bam files were supplied to Diffbind. However, it failed to generate the greylist. It is something about my bam files? The bam files are having ensembl chromosome

DiffBind

updated 18 months ago • kyliecode

I wanted to know, is it somehow possible to annotate the MA plot of only promoter peaks? I know DiffBind doesn't have built in annotation functionality, but has someone attempted to do this kind of graphs? I can imagine

diffbind chipseq rorystark

updated 4.8 years ago • bioinfouser2

Hi, I did an analysis using DiffBind in June 2022 with no errors. I restarted the project last week after updating R and DiffBind and now the normalization...I mentioned above, with an earlier R version (R version 4.1.2 (2021-11-01) -- "Bird Hippie") and DiffBind version (not sure which one) on exactly the same BAM files with the same code I did not have this problem. However, I would

DiffBind Blacklist

updated 2.1 years ago • Romain

at="" mail.utoronto.ca=""> wrote: >Hi Rory, > >I was hoping you could help with with two DiffBind questions: > >1) Is it possible to adjust the p-value / FDR threshold for the >dba.analyze function ? > >2) Is it possible

DiffBind DiffBind

updated 11.1 years ago • Rory Stark

Hi, I have run Diffbind on a set of ChIP-seq samples and generated a dba.count object. Now, I want to count reads on a set of peaks (promoters...Hi, I have run Diffbind on a set of ChIP-seq samples and generated a dba.count object. Now, I want to count reads on a set of peaks (promoters/enhancers

diffbind chipseq

updated 8.1 years ago • tangming2005

Hi everyone, I am having a small problem with Diffbind, after successfully running through the diffbind algorithm and getting a GRanges object with about 1000 differential

Diffbind

updated 10.1 years ago • ben

Hello, I'm trying to run DiffBind with some new ChIP-Seq samples and I've posted my output errors below. The main error I keep encountering is that it...and they're successfully calling the correct files. I've included my R code and my error. library (DiffBind) setwd("/scratch/Samantha.nixon/Bam_bed_Ezh2Stat3/") samples <- read.csv("samplesheet_ezh2.csv") ezh2 <- dba(…

diffbind 3.5.1 3.6.1

updated 4.4 years ago • Samantha.nixon

Hello, Recently I'm trying to perform differential binding analysis of ChIP-seq data using DiffBind. I have two group samples, which are from single-end data and paired-end data respectively, and I want to detect differential...then combined them using dba.peakset function, but I got error when performed dba.analyze(). So, can DiffBind deal with single-end and paired-end data together? And what …

DiffBind ssss

updated 3.9 years ago • Xiaojie Cheng

I thought it might be worthwhile to check how well the DiffBind analysis using DESeq2 fits the assumptions needed. The data comes from ChIP-Seq. I performed a DESeq2 analysis, using...DiffBind fetched a DESeq2 object from its results, and drew the dispersion plot. ![enter image description here][1] The fitted...Seq one should be worried if such a graph would be produced. How worrisome is…

DESeq2 DiffBind

updated 3.6 years ago • Sam

div class="preformatted">Hi all, I am trying to use DiffBind to compare peaks called in control vs condition. I have 2 replicates for each and I've also called peaks using 2 different...path (and the same for the conditions) My plan was to load all the data and then using diffbind selecte a set of common peaks for the peak callers before proceeding with the analysis. However, when I load the…

Genetics DiffBind Genetics DiffBind

updated 12.2 years ago • António Miguel de Jesus Domingues

I'm using DiffBind for ATAC-seq DA analysis. The MA plot and volcano look nothing like I expect. I do not expect a large difference between...adjusting the offset, the plots look even worse! ![loess_fail][3] I'm fairly new to both ATAC and DiffBind, so any help and tips would be greatly appreciated! ``` > sessionInfo() R version 4.2.1 (2022-06-23) Platform: x86_64-apple

DiffBind

updated 17 months ago • David.Atkinson2

Hello, I am now using DiffBind (3.0.14) to analyze my ATAC-seq data. I have two groups of samples that have drastically different peaks numbers called...The analysis method I used is `DBA_DESEQ2`. My first question is what is the best practice in DiffBind to deal with two data sets that have major changes in chromatin accessibility? ![non-normalized MA plot][1] ![full library...I want t…

DiffBind

updated 3.6 years ago • Shuwan

see code below to reproduce my observation. Thank you! Best, Julien   <pre> library("DiffBind”) packageVersion("DiffBind") #[1] ‘2.0.9’ meta_filt <- read.table("meta_2_replicates.txt",header=T) d <- dba(sampleSheet

diffbind dba.count summits

updated 7.9 years ago • julien.bryois

I'm currently using esATAC to process a number of ATAC-Seq samples that are done in two biological replicates across four sample groups. I'm interested in using DiffBind to calculate read counts from the resulting *PeakCallingFseq.bed* and *Bowtie2Mapping.bam* files. Ultimately, I...that are done in two biological replicates across four sample groups. I'm interested in using DiffBind to calcula…

esATAC edgeR DiffBind

updated 4.1 years ago • Timothy

div class="preformatted">Hi I'm testing DiffBind using a contrast between two groups containing only one sample each. According to the manual, this is highly discouraged

DiffBind DiffBind

updated 11.1 years ago • Giuseppe Gallone

Hello, I am new to DiffBind. I am trying to use dba.count, where ELSDiff is the dba Object after reading the .csv file: ``` ELSDiff <- dba.count(ELSDiff

DiffBind

updated 23 months ago • narzouni

Hi, I've used DiffBind to analyze differential binding analysis for cut&tag data. The result is showed in MAplot: ![enter image description...Hi, I've used DiffBind to analyze differential binding analysis for cut&tag data. The result is showed in MAplot: ![enter image description here][1] I noticed some peaks with 0 log fold change are differentially biding sites, while it…

DiffBind

updated 19 months ago • Ti

Dear colleagues, I'm using DiffBind for the first time and I'm encountering some issues, one in particular is quite weird. I've got a simple experiment...Dear colleagues, I'm using DiffBind for the first time and I'm encountering some issues, one in particular is quite weird. I've got a simple experiment, 3

DiffBind Reads MACS2 FullLibSize

updated 3 months ago • Marianna

<div class="preformatted"> I am trying to understand what DiffBind is doing. Notice that I executed exactly the same command on the same data twice and got different counts. counts=dba.count...div class="preformatted"> I am trying to understand what DiffBind is doing. Notice that I executed exactly the same command on the same data twice and got different counts. counts

DiffBind DiffBind

updated 10.7 years ago • Naomi Altman

Hello, I am running Diffbind for Cut&Run data. It is from rare types of tumors that unfortunately was not possible to create replicates. However

DiffBind

updated 3.4 years ago • Danielle

amp; many thanks, Gary > setwd("/Volumes/NCHU/20170811\_Tang\_MandarinDuck/20170815\_analysis/diffbind") > require("DiffBind") Loading required package: DiffBind Loading required package: GenomicRanges Loading required

diffbind

updated 7.2 years ago • Gary

Hello, I am using DiffBind for my MeRIPSeq (mRNA methylation) analysis. <span style="line-height:1.6">I have been using it to extract a consensus

diffbind peak chipseq

updated 8.4 years ago • becavin.christophe

answers to each post are extremely helpful. However, I feel confused to some results while running DiffBind. To better illustrate my problems, I would like to invite you to go through my case. library("DiffBind") samples=read.csv

DiffBind

updated 2.0 years ago • littlefishes20

Hi  I am new to R and to DiffBind. I am trying to analyse some ChipSeq data. I have aligned reads to the genome and obtained a bam and bed file. Then I obtained...Hi  I am new to R and to DiffBind. I am trying to analyse some ChipSeq data. I have aligned reads to the genome and obtained a bam and bed file. Then I obtained peak calls using MACS. __While using diffbinds, I am g…

R DiffBind

updated 7.8 years ago • hemantgujar14

UCSC/IGV to determine the proper binding patterns, this is still rather troubling to me as I like diffbind. Any ideas to what could be going on? Thanks very much for any help! Chris

diffbind

updated 8.0 years ago • cnova1950

Hi, I'm using Diffbind for obtaining differential binding patterns for a bunch of samples. I was wondering how I could have all the samples...pre> ESR1_mutation_db_T47D <- dba(sampleSheet="C:/Users/seb10/Box Sync/esr1-mut/ChIP-seq data/Diffbind/Running_DiffBind/Meta_data_T47D.csv") ESR1_mutation_cr_T47D <- dba.count(ESR1_mutation_db_T47D, summits

diffbind heatmap correlation

updated 7.7 years ago • a.bahraini88

gene in the diseased group is more accessible than the control group? The object is created from the DiffBind package. Thank you so much! ![enter image description here][1] ![enter image description here][2] [1]: /media/images/a55c87a4

DiffBind ATACSeq

updated 19 months ago • Chris

Hi! I have 9 samples (each condition has three samples). I am running diffbind as follows: dbind<-dba(sampleSheet = "diffbind.csv") dbind_consensus <- dba.peakset(dbind, consensus=c(DBA_TISSUE

diffbind

updated 4.1 years ago • alessandro.testori

Hi, I am performing DiffBind on ATACseq data and I have a question regarding the use of block and design in setting a dba.contrast. From a previous

DiffBind R ATACSeq

updated 3.4 years ago • fleur_p90

Hello, I am using DiffBind and I find it very useful and straightforward to run. However, after running a few trials, I seem to get very different

DiffBind macs2

updated 5.7 years ago • Anna

div class="preformatted"> Hello! I am using the DiffBind package to search for differences in histone modifications of ChIPseq peak data, I created a .csv files using sorted.bam

ChIPSeq chipseq DiffBind ChIPSeq chipseq DiffBind

updated 10.6 years ago • Guest User

Hello, I'm using `` DiffBind `` version 2.6.6 to do ChIP-seq differential binding analysis for a transcription factor that binds at genes transcription...a bed file with peaks that are centred on the TSS and all have 2500bp width. Now, when I move to `` DiffBind `` for the differential analysis I used the function `` dba.count() `` with the parameter `` summits `` set to 1250 since I've read

diffbind chipseq counts peaks bedtools

updated 3.6 years ago • Ni-Ar

Hi, I am having some trouble in retrieving the results of a Differential Analysis using Diffbind. In particular, when I use the function dba,report() with the option *bflip=TRUE or FALSE* I do not see any change in the...Hi, I am having some trouble in retrieving the results of a Differential Analysis using Diffbind. In particular, when I use the function dba,report() with the optio…

bflip dba.report DiffBind

updated 3.3 years ago • Riba Michela

gt; wrote: Dear Rory I'm contacting you to know your thoughts on the possibility of using DiffBind with a Chip-exo dataset. The dataset is composed of transcription factor binding data for a large number of hapmap

HapMap HapMap

updated 11.4 years ago • Rory Stark

Hello All, I am receiving an error when inputing my data into DiffBind...dba(sampleSheet="TCGA\_DiffBind.csv").  I have created a sample sheet file as described in the Diffbind tutorial...cvs file using...write.csv(TCGA\_4, "TCGA\_DiffBind.csv", row.names = F) and then read the file into DiffBind using...dba(sampleSheet="TCGA\_DiffBind.csv") but get the follow error.  M026 SK…

diffbind

updated 8.5 years ago • cnova1950

the initial correlation heatmaps indicate that they are quite far apart. As a result, when I use DiffBind, I don't see more than 1 differential binding site with default FDR. So, I set `th=1` to get the full report. However, my question

DiffBind ATACseq replicate

updated 4.0 years ago • CodeAway

I have differential binding analysis performed on a set of samples and plotted a Venn diagram (using DiffBind) to look at overlapping and unique diff. bound sites. Now I want to get those peaks in the Venn Diagram as a list for further

DiffBind plotvenn

updated 6.6 years ago • Hesh

the following allowable factors: Tissue Factor Condition Treatment Replicate Caller library(DiffBind) dba_obj <- dba(sampleSheet = "sample_sheet.csv") dba_obj <- dba.blacklist(dba_obj, blacklist = DBA_BLACKLIST_HG38

DiffBind ATACSeq

updated 4 weeks ago • Alpesh Querer

Hello, I'm trying to run DiffBind on my CUT&RUN data to get the differentially bound peaks between two conditions (DMSO and inhibitor). In sample_sheet.csv

DiffBind DESeq2

updated 11 months ago • Miquel

the batch effects in the model by blocking them as a factor. Thus, I decided to use DiffBind, edgeR and DESeq2 and their respective procedures for blocking factors. My results are different for the different...tools and using the same matrix of read counts provided by DiffBind. I found some details about how the [ single-factor analysis using edgeR](https://sup…

diffbind

updated 8.7 years ago • armandorp

Hi, DiffBind is great and a heat map of counting reads is very helpful (e.g. the attached figure). However, I would like to run a hierarchical

DiffBind

updated 9.1 years ago • Gary

Hello everybody, I would like to do a heatmap of selected genes for my ATAC-seq data. When I use DiffBind and I do dba.PlotHeatmap of my differentially accessible regions I get a full heatmap of all the regions and all

DiffBind

updated 3.2 years ago • Laura

I'm pretty new to ATAC-Seq analysis so I'm sorry if my question is dumb. I did read through the DiffBind vignette and I see that Deseq2 was said to be more preferred. When I tried running my data using both EdgeR and Deseq2

DiffBind edgeR ATACSeq DESeq2

updated 10 months ago • Jawahar

Hi, I am facing a problem using diffBind version 1.12.3 (see sessionInfo below). when running dba.count, I get an error > x <- dba.count(x,minOverlap = 1,score

diffbind

updated 9.6 years ago • carl.m.herrmann

Hello all, when I use dba.plotVenn to get diagrams of my peaksets using DiffBind the Intervals numbers don't match the Venn diagram. > tumors <- dba(sampleSheet='file.csv',minOverlap=F) AFTER001

diffbind

updated 10.1 years ago • t.severson

In [this post][1] I have described that DiffBind gives a different number of DE genes when using dba.analyze, and when returning the results as a DESeq2 object. It...seems that I have found the reason. Underlying that is DiffBind (at least by default) not using DESeq2's MLE estimation when calculating (log) fold change. So the concentration of...DiffBind equals precisely log2(mean across conditi…

DiffBind

updated 3.6 years ago • Sam

Hi everone, Have you ever seen "diffbind DESeq2 analysis has not been run for this contrast" during DiffBind analysis (during: plot(K9\_broad\_affinity...Hi everone, Have you ever seen "diffbind DESeq2 analysis has not been run for this contrast" during DiffBind analysis (during: plot(K9\_broad\_affinity, contrast=1)) __I've confirmed DiffBind is workable using the test data …

DiffBind R chipseq

updated 7.2 years ago • kyliecode

32:10 -0400 To: Rory Stark <rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>> Subject: DiffBind, dba.count result object Hi I have a question about the content of the dba.count result object. There is "sites" element

DiffBind DiffBind

updated 10.5 years ago • Rory Stark

seem to be able to do the same for the clustered heatmap (the one produced by plot(results) in DiffBind). plot(results,vColors=mypalette) or plot(results,col=mypalette) does not work. It says "error in plot.new() figure margins

DiffBind plot color

updated 4.9 years ago • melnuesch

Hi, I am trying to use the DiffBind package but I get the following error: ``` wtvspq.count = dba.count(wtvspq[1:2], bParallel = FALSE) Computing summits... Error...changing the config to RunParallel=FALSE, I get the same error. I had problems in the past using DiffBind on Windows, but at least I was able to run it serially. ``` wtvspq = dba(sampleSheet="reduced.csv", dir="C:/DATA/BAM_as_BED/",…

parallel R DiffBind

updated 3.3 years ago • eggrandio

condition A. However, I get half the peaks up and half down. That does not make sense. I am using DiffBind. My first instinct was that the peaks were being normalized, so in condition B (where there are few reads in the peak

diffbind

updated 9.2 years ago • igor

span style="line-height:1.6">Hi Rory,</span> I was wondering whether Diffbind could call differential peaks from bed file? The reason I ask this is that if I would like to all differential peaks...from two sets of diffPeaks called by diffBind. For example, I have group1, group2, group3, group4. Then I already used diffbind to call differential Peaks. Diffpeak1...diffbind(group1,group2…

diffbind

updated 9.6 years ago • yijing.su

Hi, I am running Diffbind differential analysis of ATAC-seq samples. I am testing out the different options in diffbind and I could successfully...KO3_TCDF_peaks.narrowPeak,narrow My code is ``` # mamba install bioconda::bioconductor-diffbind library(DiffBind) SAMPLESHEET="samplesheet_PE_q0.05.csv" # Minimum overlap for the samples to build the consensus

DiffBind

updated 10 months ago • Aswathy

2013-06-19 15:23, "Lawson, Nathan" <nathan.lawson at="" umassmed.edu=""> wrote: > >I am using DiffBind to identify differentially occupied elements from >histone modification ChIP-Seq between two different cell...Again, these datasets were successfully entered as a dba object and >subsequently analyzed using DiffBind on my computer. The original input >f…

DiffBind DiffBind

updated 11.5 years ago • Gord Brown

Hello, I receive a error message when running the dba.count() in Diffbind. SCFIL = dba.count(SCFIL, minOverlap = 1) __Fehler in if (res\[i\] == -1) { : Fehlender Wert, wo TRUE/FALSE nötig ist__ The DBA file looks

diffbind

updated 9.0 years ago • yu.fu

Hi,  I have two questions about how DiffBind works (listed below).  Could you hep me figure these out. Thank you for your help in advance!  Best, Duygu Ucar...Hi,  I have two questions about how DiffBind works (listed below).  Could you hep me figure these out. Thank you for your help in advance!  Best, Duygu Ucar.&nbsp

diffbind normalization

updated 9.9 years ago • ucarduygu

Hi, I am trying to run DiffBind using parallel execution but it does not detect multiple cores, although I can through: <pre> > parallel::detectCores...1] 8</pre> When I try to run DiffBind. Here's what I see with a test run: <pre> > test = dba(sampleSheet = "TEST.xls") wt_D_1 wt D 1 bayes wt_D_2 wt D 2 bayes > test.counts...datasets  m…

diffbind parallel biocparallel

updated 6.9 years ago • eggrandio

Hi Rory, I am using DiffBind to analyze differential transcription factor binding in some data I have and I keep getting the message as a result

diffbind p-value differential binding analysis fold enrichment values using diffbind

updated 8.5 years ago • alisonhanh.nguyen

One of the changes from DiffBind 1.12.3 to DiffBind 1.14.0 is at line 1045 of analyze.R, where the line: <pre> idx = match(as.integer(sites),1:nrow(pv$allvectors

DiffBind edgeR

updated 9.6 years ago • Aaron Lun

HI All, I have been using DiffBind for several analyses. <span style="line-height:1.6">But lately I am having problems with a dataset. </span><span...or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(DiffBind) Loading required package: GenomicRanges Loading required package: BiocGenerics Loading requir…

diffbind dba.count

updated 8.5 years ago • em540