Bioconductor Forum

I am retrieving the normalized counts of reads in peaks (scores) from DiffBind, as explained in [this][1] Bioconductor post : ``` dba.peakset(dbObj_norm, bRetrieve=TRUE ) %>% as.data.frame() %>% head() seqnames

DiffBind

updated 8 months ago • Sam

with the conditions (such that all the samples in some batches have the same condition). By default, DiffBind handles the most straightforward cases where the blocking effect includes samples on both sides of the primary...at="" dpag.ox.ac.uk=""> >To: bioconductor at r-project.org >Subject: Re: [BioC] [DIFFBIND] batch effects and blocking factors >Message-ID: <53A94…

DiffBind DiffBind

updated 10.4 years ago • Rory Stark

Dear all, I'm using DiffBind to compare histone modifications in two groups of samples. I'm comparing two cell-types, from the same 8 individuals...Dear all, I'm using DiffBind to compare histone modifications in two groups of samples. I'm comparing two cell-types, from the same 8 individuals. So I have 16 samples, 8 of each cell-type. The aim is to find peaks that are significantly diferent…

diffbind chip-seq

updated 8.2 years ago • D.Hemerich

I'm using diffbind to identify differential binding of CUT&tag peaks of H3K27ac. I obtained scaling factors from ChIPSeqSpikeIn...package. I'm very new to bioinformatic analysis. I know the Diffbind has dba.normalize function which you can specify a numeric normalization factor. Could anyone suggest the code...to specify number for normalization method in dba.normalize using DiffBind? Tha…

DiffBind CUT&Tag

updated 11 months ago • Hai

div class="preformatted"> Hello, I'm using DiffBind version 1.2.0 with R 2.15.0 on linux. I've created a dba object data.deseq and run: > data.deseq = dba.count(data.deseq

a4 DiffBind a4 DiffBind

updated 12.4 years ago • Elisabetta Manduchi

Hi, I am trying to read a DBA object from a Samplesheet but DiffBind throws me an error despite having the file paths correctly set. ``` library(DiffBind) setwd("C:/Users/alexa/Documents/HKU

DiffBind

updated 3.4 years ago • Alexandre

I attempted the run DiffBind (v3.4.0) for my samples ( I have bam, control bam and peak files in the sample sheet). After running about 5 hrs, it returns

DiffBind ChIPSeqData

updated 3.0 years ago • sfpacman

Hello, I want to create a ChIP heatmap using profileplyr, but I want to merge some samples according to condition. This is implemented in DiffBind by the looks of things, but I want to customise the heatmap a bit to show the conserved peaks, gained peaks, and lost peaks in the same plot (from what I can tell, DiffBind only shows gains and losses). I also want to be able to combine all sampl…

DiffBind profileplyr

updated 4 months ago • jesswhitts

hi  Rory, I'm a new with DiffBind for d<span style="background-color:rgba(0, 0, 0, 0)">ifferential binding analysis of ChIP-Seq peak

DiffBind differential binding analysis

updated 9.2 years ago • February

Hi Rory, I am using DiffBind to identify sites differentially bound (affinity analysis) by a transcription factor in control (WT), heterozygous...used both default normalization method and spike in normalization. The results are similar for both. DiffBind identifies a good number of sites that are significantly differentially bound between WT and KO. Comparing HET

DiffBind

updated 2.5 years ago • ipsc-jl

Hej Rory, Gord! I get an error message from DiffBind dba.peakset when trying to derive a consensus peakset. The error is: Error in if (res >= minval) {: missing value where...Hej Rory, Gord! I get an error message from DiffBind dba.peakset when trying to derive a consensus peakset. The error is: Error in if (res >= minval) {: missing value where TRUE/FALSE needed. I have tracke…

software error chipseq diffbind

updated 9.6 years ago • Nicolas Delhomme

So I output a matrix from DiffBind as my input into DESeq2, with the chromosome positions being removed from the count matrix, just leaving the first...and adjusted p-val so I was wondering how I can remap this list to the original matrix output from DiffBind so I can recover the chromosome positions since this contains only the key.  Thanks! &nbsp

deseq2 deseq diffbind differential binding analysis

updated 7.0 years ago • rbronste

Hi, I am using DiffBind (development version 3.0.5) to identify differential open chromatin regions in two cell groups (control vs treated

DiffBind

updated 3.6 years ago • Bei Jun

2013 4:05 AM >To: mzinkgraf at gmail.com >Cc: bioconductor at r-project.org >Subject: Re: DiffBind and GRanges error extracting overlapping peaks >using dba.overlap > >Hi Matt- > >Your code looks good -- this...as I can't reproduce it >with some datasets I have. > >Is there a way you can share the DiffBind Object ("chip"…

DiffBind DiffBind

updated 11.1 years ago • Rory Stark

but things are not going smoothly. The loading of the samples seem to be ok: ############# library(DiffBind) H3K4m3 = dba(sampleSheet="samplesheet_all.csv") H3K4m3 # 8 Samples, 19885 sites in matrix (24260 total): # ID Tissue Factor

GO BSgenome BSgenome GO BSgenome BSgenome

updated 11.8 years ago • António Miguel de Jesus Domingues

I am using Diffbind for an ATAC-Seq analysis. My peak caller is MACS2, and here is my sample sheet:** ![my sample sheet][1] **I run Diffbind with the...idea about this? Thank you so much!** ``` library(BiocParallel) register(SerialParam()) library(DiffBind) data <- dba(sampleSheet="sampleSheet.csv") data <- dba.blacklist(data, blacklist=DBA_BLACKLIST_GRCH38, greylist

dba.count DiffBind ATACSeq

updated 14 months ago • sophie.hfliu

Hi, Recently I'm using DiffBind. After running dba.count, I can use tamoxifen$binding to get a table. > head(tamoxifen$binding)   CHR &nbsp...Hi, Recently I'm using DiffBind. After running dba.count, I can use tamoxifen$binding to get a table. > head(tamoxifen$binding)   CHR  START...nbsp;18.2079750  21.83680 &…

diffbind ChIP-seq

updated 8.4 years ago • xie186

equal to the number of peaks that I had in my input file. When I went back to the tutorial of the DiffBind package ( http://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf ), I found the same

diffbind

updated 10.0 years ago • Silvia

running the same code without peaks=NULL, score=DBA_SCORE_READS I am using R version 4.3.1 and DiffBind 3.10.1. Help is very much appreciated

DiffBind ATACSeq

updated 10 months ago • isaromero8888

Hello, I'm running a differential expression profile for a protein using diffbind. I'm curious about one thing, it's not really a problem per se, but the documentation is unclear about a specific part...and the analyze it under the same parameters, I get a different set of results: ```r library(DiffBind) library(tidyverse) library(rtracklayer) library(dplyr) library(stringr) library(BiocParalle…

DifferentialExpression DiffBind

updated 2.5 years ago • Luca

I am trying to analyse a ChIP-Seq data set with `DiffBind`. These are the contents of my sample sheet ("diffbind_samples.csv"): ``` SampleID,Tissue,Factor,Condition,Treatment,Replicate...I am trying to analyse a ChIP-Seq data set with `DiffBind`. These are the contents of my sample sheet ("diffbind_samples.csv"): ``` SampleID,Tissue,Factor,Condition,Treatment

DiffBind

updated 2.7 years ago • nw416

Hello, I d like to see the analysis of DiffBind for my peakset and alignment files with 2 Replicates but I have a frustratingly repeated Error saying : <pre> `Error...would be really helpful. I am working on R version 3.4.2 (2017-09-28) -- "Short Summer", with DiffBind v2.6.6  in Ubuntu 16.04. Here is my csv file : <table align="center" border="1" cellpadding="1" cellspaci…

diffbind chipseq peaks dba is.na

updated 6.6 years ago • maria.kondili

narrow``` Here is the code for DiffBind Analysis ```r library(DiffBind) treg=dba(sampleSheet="PS_Treg_atacseq-1.csv") treg=dba.count(treg,bUseSummarizeOverlaps

ATACSeq DiffBind

updated 3.8 years ago • Asma

Hi everyone, I am running into this error with DiffBind that I have not had before.It is happening with multiple datasets. I have found similar threads with this issue...Hi everyone, I am running into this error with DiffBind that I have not had before.It is happening with multiple datasets. I have found similar threads with this issue but

BiocParallel BiocPa DiffBind

updated 2.8 years ago • r.finn

nbsp;methods   \[9\] base      other attached packages:  \[1\] DiffBind\_1.16.3            RSQLite\_1.0.0              DBI\_0.3.1     &nbsp

diffbind dba.overlap

updated 8.7 years ago • Udi Landau

Dear Developers, Thank you for the nice software! I am using DiffBind for merging peaks and re-counting the reads in the consensus regions and have a few questions about diffBind. 1. the

DiffBind

updated 4.0 years ago • Tongjun

dba.count, however. Here is what I have done.  1. I have update all the packages. when loading Diffbind 2.6, there is no warnings. 2. Then I run dba.count using  <span style="background-color:rgb(245, 245, 245)">summits...style="background-color:rgb(245, 245, 245)">Many Thanks</span> Zhaolin  <pre> > library(DiffBind) Loading r…

diffbind dba.count summits

updated 3.9 years ago • zhaolin20042008

Hi, I have generated a heatmap based on binding sites using DiffBind package. I was wondering if it is possible to output the rows (dendogram) in the order as they appear on the heatmap...Hi, I have generated a heatmap based on binding sites using DiffBind package. I was wondering if it is possible to output the rows (dendogram) in the order as they appear on the heatmap. Many

diffbind

updated 8.3 years ago • svohra

Hello I have a question regarding DiffBind analyzing of ATACseq data . I have ATACseq counts of control and case samples in a reference peak set as a count matrix...sample IDs,I do not have access to bam files nor peak calls of these samples . Is it possible to use DiffBind to identify regions that are differentially accessible between case and control ? if so how can I construct a DBA

ChIPSeq ATACSeq differentially_occupied DiffBind

updated 3.4 years ago • pegah.taklifi

Hello, I've been having a fair amount of trouble trying to create a dba object in diffbind from a .csv samplesheet. I used this code before, but I'm reanalyzing some data and I keep getting the error : "Error in...Hello, I've been having a fair amount of trouble trying to create a dba object in diffbind from a .csv samplesheet. I used this code before, but I'm reanalyzing some data and I keep …

DiffBind DifferentialPeakCalling

updated 5 months ago • Mallory

Hi all, I'm using DiffBind 3.2.14 with spike-in data. I have an issue when running dba.normalize(). The error seems to be coming from the minQCth

DiffBind

updated 3.3 years ago • jseg

Hello, Using DiffBind, I would like to get the peaks in common between the edgeR approach and the DESeq2 approach. With the edgeR approach

DiffBind

updated 3.4 years ago • etiennedanis

Dear support, I got an bgzf_read error while running diffbind dba.count(). I had posted the message here for the reference, could anyone kindly provide any advises? Thank you in...Dear support, I got an bgzf_read error while running diffbind dba.count(). I had posted the message here for the reference, could anyone kindly provide any advises? Thank you in advance

diffbind

updated 5.1 years ago • Kath

I used the Diffbind to analyze the ATACseq data, which get from different time point. I want to find out how the peaks changing by time...I used the Diffbind to analyze the ATACseq data, which get from different time point. I want to find out how the peaks changing by time, and

diffbind

updated 4.2 years ago • qq809825706

at="" dpag.ox.ac.uk=""> wrote: >Hi Rory > >I have a further question about DiffBind. Could you tell me something >more about the clustering visualisation obtained with >dba.plotHeatmap(....correlations

Sequencing GO Clustering GLAD edgeR DESeq DiffBind Sequencing GO Clustering GLAD edgeR

updated 11.3 years ago • Rory Stark

Hi I have a question about diffbind counts. I read in the vignette that the binding affinity matrix contains a ___normalized___ read count for each

diffbind

updated 9.6 years ago • mm2489

Seq data. However, there is an error message when I would like to estimate their FRiP values using DiffBind below (i.e., Error in if (colnames(res)[i] == "Peak caller") { : argument is of length zero). Could you help me? Many thanks. Best, Gary

DiffBind FRiP ATAC-Seq dba.show dba.count

updated 5.7 years ago • Gary

Hi    I am a user of DiffBind and I'm having a hard time trying to export the result of dba.count as a data frame. Basically, I need a table of consensus

diffbind

updated 9.6 years ago • mm2489

Hi all, I'm new to **diffbind**. I've been given a set of **ATAC-seq** data computed with [nf-core/atacseq][1] and asked if there is any peak associated with

DiffBind ATACSeq

updated 8 months ago • Pierre Lindenbaum

Hi: I am using DiffBind to analysis some hMeDIP-seq data. I have called peak from MACS2 (narrow) and SICER (broad) separately. And the results...can both be loaded into DiffBind. I like to generate AffinifyBinding matrix for custom downstream analysis and visualisation, as it returns nice

Peaks MAC2 DiffBind

updated 3.4 years ago • Yuan Tian

Hi Rory, I have just recently starting using DiffBind and was hoping you could help me clarify something. Regarding filtering peaks with few counts, i was wondering if

diffbind

updated 9.5 years ago • mc.suciu

Hi, I was wondering if anyone would be able to help. I was using the previous version of DiffBind v3.0.7 to successfully analyse ChIP-Rx (ChIP-seq with a 'spike in' genome) with the same sample sheet included below

ChIP-Rx DiffBind chipseq

updated 4.0 years ago • indi97

not, I will remove this post. I have a principal component analysis (PCA) figure below produced by DiffBind. After discussing with my colleagues, we wonder why the variation of Principal Component \#1 is smaller than Principal...3 --tsize 75 --nomodel --extsize 200 --qvalue 0.00001 --slocal 1000 --llocal 10000 --cutoff-analysis `` DiffBind commands I used `` > h3k27ac <- dba(samp…

diffbind PCA

updated 7.2 years ago • Gary

4 treated and input pairs. I am running the analysis on AWS EC2 in which I have installed r-base and DiffBind **in a conda environment**. I am currently trying to resolve the following issue from dba.analyze: ```r > h3k27ac <- dba.analyze

DiffBind

updated 3.4 years ago • kwangbom

a large scale opening of the chromatin in the KD. After calling Peaks with MACS2 and running the DiffBind steps, I used 3 different Normalization commands to see how or whether they differ significantly in terms of numbers

DiffBind

updated 4.0 years ago • Debayan

Hi All, I`m using diffBind to analyze my ATACseq results. I have 2 groups (before and after treatment) in triplicates. How can I create a plot of...per sample. Currently I used soGGi package (attached), but I wish to use the data from the diffBind dba.obj and compare it to soGGi. Thank you ! nucFree <- regionPlot(bamFile = files[[3]], testRanges = TSSs, style = "point", …

DiffBind ATACSeq

updated 11 months ago • inna.gur

I used diffbind to analysis the data with 5 time point. I wanted to find out the unique peaks in different time point. so I run the code

diffbind

updated 4.1 years ago • qq809825706

Hi,  I have histone, broad-peak data, however some of the peaks are actually rather narrow. So what I can see happening is that the broader peaks are being nicely identified as differentially expressed by diffbind, but the narrow peaks which seem highly up-regulated (with big fold changes) are not reaching FDR significance. My interpretation...see happening is that the broader peaks are…

diffbind r chipseq

updated 7.2 years ago • reubenmcgregor88

Hi! Have a question about using DiffBind for ChIP-seq data with drosophila spike-ins. I already have computed peaks from usage of control data and spike-in...adjustment based on minimum). Is there an easy way to use these computed coefficients for the DiffBind analysis? I found [this post,][2] but there is a link to pipeline which starts from reads, while I would like only to correct

DiffBind Chipseq spike-ins

updated 4.1 years ago • Konstantin Okonechnikov

Hi all, I have a question about generation a path in R with a file in a windows path. Currently I am using this path for a bamfile counting reads for DiffBind: bamReads = "U:/R/win-library/3.0/Data\_ChIP\_Experiment/aligned\_S00D47H1-RUNX1.filtered.bam" This does not work at...in R with a file in a windows path. Currently I am using this path for a bamfile counting reads for DiffBind: bamRe…

bioconductor R windows diffbind

updated 7.6 years ago • jorrenkuster

genrich by merging case and control sampes. I am having two narropeak files. Now, I am trying to use diffbind for identifying differtial peaks. But I am have the following error whole running `dba.count`. I am not sure why I am

DiffBind Genrich

updated 4.0 years ago • peris_baba

Hi everyone, I'm using DiffBind to analyse some H3K4me3 ChIP-seq data. I've used DiffBind for H3K27ac ChIP-seq data as well, and when I drew MA plots using...concentrations (see attached figure). When I use these data for differential binding analysis with DiffBind's default settings, both these groups (low conc/positive LFC and high conc/negative LFC) contain lots of differentially

DiffBind MA plot normalization ChIP-seq

updated 4.4 years ago • hasse.bossenbroek

1083 1297 ``` by the way, I find it is hard to open the link posted in the DiffBind manual. > http://https//www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/diffbind Best wishes

DiffBind

updated 3.8 years ago • shangguandong1996

Hi! I have been trying to run diffbind with count tables I generated for each replicate. I also normalized the read counts by subtracting the counts from

diffbind IRanges

updated 5.3 years ago • akutsch

Dear dr. Stark and community, I'm using Diffbind to obtain differential expression values for a series of interesting regions and I have some questions.I run...Dear dr. Stark and community, I'm using Diffbind to obtain differential expression values for a series of interesting regions and I have some questions.I run the

diffbind normalization

updated 9.5 years ago • eva.pinatel

K27ac, and K4me1. We carried out peak calling using SEACR and then differential peak calling using Diffbind. Now, we want to go back to the raw peak data and just plot the normalized peak data. Can i use the dba.normalize function...to ChipSeeker so I can plot it. I don't know if this is a naive question because I went through the diffbind tutorial and couldn't find anything specific to normalizi…

Normalization Peakdata DiffBind Cut&Tag

updated 2.2 years ago • bhandary.8590

Hi,  I am having some trouble with the dba.count function in Diffbind dba.count function. See below:  <pre> DBA.count = dba.count(DBA, bUseSummarizeOverlaps = FALSE, mapQCth = 30, bCorPlot

diffbind

updated 6.1 years ago • loretta

<div class="preformatted"> Hello I am using DiffBind to identify consensus binding sites for multiple transcription factors that have biological replicates. In addition...div class="preformatted"> Hello I am using DiffBind to identify consensus binding sites for multiple transcription factors that have biological replicates. In

DiffBind DiffBind

updated 11.1 years ago • Guest User

with the Encode ATACseq pipeline. I now want to call differentially opened chromatin regions with DiffBind, but it gives me an error when I want to normalize. Also when I run dba.analyze, it gives me the same error. I don't understand...what I am doing wrong? I appreciate any input! best, Ben ```r library(DiffBind) dir <- "/staging/leuven/stg_00072/Ben/ATACseq" setwd(dir) ## read in …

DiffBind

updated 3.5 years ago • ben.vanderveer

Hey, I saved a first chipQC object using consensus=TRUE,bCounts=TRUE,summits=250 options. Then I reused it latter inside DiffBind. __First I was wondering if it uses score or count to make heatmap ? Documentation it misleading, it is said it uses scores...chipQC object using consensus=TRUE,bCounts=TRUE,summits=250 options. Then I reused it latter inside DiffBind. __First I was wondering if i…

diffbind

updated 7.2 years ago • ZheFrench