Bioconductor Forum

respective normalisation factors exactly, or the inverse of the normalization factors generated from diffBind? Thank you! ================ Codes: ```r library(DiffBind) library(edgeR) library(tidyverse) library(dplyr) samples <- read.csv('Sample.csv

DiffBind

updated 7 months ago • Henry

Dear friends, I have been using diffbind to get RLE/TMM normalized counts. I have noticed that the RLE/TMM normalization is performed based on reads subtracted...I have tried following by setting `bSubControl = F`, but it does not work. ```r library(DiffBind) library(tidyverse) h3k27ac_samples <- read.csv("h3k27ac.csv") #use sorted bam h3k27ac <- dba(sampleSheet=h3k27ac_samples

DiffBind

updated 2.5 years ago • ksong

Hi all, I am having trouble getting DiffBind's dba.counts to run to completion. I am frequently met with the following error: ```r Reads will be counted as Paired...Hi all, I am having trouble getting DiffBind's dba.counts to run to completion. I am frequently met with the following error: ```r Reads will be counted as Paired-end...I suspect is problematic. Code should be placed in three bac…

DiffBind

updated 3.2 years ago • rreese2

in the final matrices, to the extent that it's stronger than my treatment effects. I'd like to use DiffBind's blocking function to account for that. The contrasts I wish to conduct all involve a subset of the data- which works...fine without blocking. Say 'diffbind\_count' is a DBA on which I've conducted the couting step, the regular contrast works fine: <pre> >unname(diffbind_c…

diffbind batch effect

updated 8.3 years ago • Jon Manning

release (https://bioconductor.org/news/bioc_3_11_release/) . ```r > BiocManager::install("DiffBind") Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24) Installing package(s) 'DiffBind' also installing...pc-linux-gnu-library/4.0/systemPipeR’ ERROR: dependency ‘systemPipeR’ is not available for package ‘DiffBind’ * removing ‘<path>/R/x86_64-pc-linux-gnu-library/4.0…

systemPipeR Bioconductor DiffBind BiocGenerics

updated 3.8 years ago • tina

Hi Everyone: I want to analyze 5hmC(from hMeDIP-seq) with DiffBind. I want to analyse both Narrow and Broad peaks for 5hmC. I have some questions: ### 1. Best way to call Narrow/Broad peaks...Hi Everyone: I want to analyze 5hmC(from hMeDIP-seq) with DiffBind. I want to analyse both Narrow and Broad peaks for 5hmC. I have some questions: ### 1. Best way to call Narrow/Broad peaks? Usin…

ChIPSeq SICER2 DiffBind MACS2 offtopic

updated 3.5 years ago • Yuan Tian

hundreds of reads, then there is a meaningful (significant) difference. The bottom line is that DiffBind is mostly designed for comparing sample groups, and not so much for comparing individual samples. Hope this helps...to get your current input >on: >From what I understand from your tutorial and emails - running DiffBind >on this dataset would basically treat it like two …

GLAD edgeR DiffBind DESeq2 GLAD edgeR DiffBind DESeq2

updated 10.7 years ago • Rory Stark

Hi DiffBind Team, I've been looking to use your package to analyse some ChIP seq data and have been following the vignette for...Hi DiffBind Team, I've been looking to use your package to analyse some ChIP seq data and have been following the vignette for guidance...two peak callers (MACS and SPP) and was hoping to treat these two sets of peaks as "replicates" in DiffBind. I'm convinced I've re…

diffbind

updated 7.1 years ago • Sophie Shaw

3.4.0 and RStudio to 1.0.143. After doing so, I noticed that when I try to read in a peakset using DiffBind, RStudio will quit unexpectedly.  The command that causes the quit: peakset = dba(sampleSheet = "expinfo.csv") The...nbsp; datasets  methods   base      other attached packages:  \[1\] DiffBind\_2.4.1   &nbsp…

software error diffbind rstudio abort quit

updated 7.6 years ago • msabbag2

Hi, I used DiffBind for a collaborator who noticed that, contrary to his expectations, a particular region (which overlaps highly significant

diffbind

updated 7.6 years ago • Silvia

Dear Dr. Stark, The following question has been asked before regarding error in dba.analyze step of diffBind when the contrast is set up for samples with no replicates. Obviously I should be comparing samples with multiple...Dear Dr. Stark, The following question has been asked before regarding error in dba.analyze step of diffBind when the contrast is set up for samples with no replicates. Obv…

diffbind

updated 9.7 years ago • danishm20

Hi everyone! When we prepare the sampleSheet matrix for the DiffBind::dba function, we may have 2 columns for bam files - 1 for ChIP bam and 1 for Input/IgG bam. Here I have 2 bam files for ChIP

DiffBind chipseq

updated 14 months ago • lin.pei26

Hi,  I have previously used the DiffBind package to successfully analyze some ChIP-Seq data, but after upgrading R (version 3.2.1) and downloading the latest...package version the dba.count() function in DiffBind (version 1.14.4) now results in the following error on a Linux machine:  --- <pre> > diffh3k4me3 = dba.count(diffh3k4me3

DiffBind

updated 9.4 years ago • Trevor

have ATAC sequencing data for two types of cells, each with three replicates. Get strange results by DiffBind analysis. Why is my volcano map only halfway？ I don't know where I went wrong. Is there a problem with the original data

ATACSeq DiffBind

updated 2.4 years ago • young

3 peaks also show up in all 6 .narrowPeak files. When I run the following code: ``` library(DiffBind) library(TxDb.Hsapiens.UCSC.hg38.knownGene) samples <- read.csv("meta/samplesheet.csv") dbH3K27ac <- dba(sampleSheet

DiffBind

updated 4.0 years ago • Sebastian

Hi I am using DiffBind's dba.plotHeatmap() or just plot() to plot a correlation matrix between the peak calls. For my correlation matrix I...Hi I am using DiffBind's dba.plotHeatmap() or just plot() to plot a correlation matrix between the peak calls. For my correlation matrix I don...labRow" matched by multiple actual arguments For details you can visit this page for DiffBind …

Diffbind plot heatmap.3

updated 5.3 years ago • researcher

Hello, I'm trying to run DiffBind with my ChIP-seq data. I do not want to subtract control reads from ChIP reads, which should be controlled by `bSubControl...64-bit) Running under: Ubuntu 16.04 LTS Matrix products: default BLAS/LAPACK: /opt/miniconda3/envs/diffbind/lib/libopenblasp-r0.3.10.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US…

DiffBind

updated 3.8 years ago • Ha

luck to find a way to mark individual element. Thank you in advance. ![Figure 11 from the DiffBind document][1] [1]: /media/images/14f59ed3-ff8e-4ef3-8a78-c39909c7

DiffBind

updated 16 months ago • Junsik

Hello, I am new to the field of bioinformatics and currently using your R package (DiffBind\_2.6.6) for the analysis of my ATAC-seq data to identify differences in chromatin accessibility between groups

Diffbind

updated 5.9 years ago • Rob Buurstede

Hi, I'm analyzing my chipseq data and am encountering some issues. I'm new to chipseq so any help is appreciated. Here is my pipeline: I have triplicates for my treatment and triplicates for control. 1) Align filtered & trimmed Illumina fastq (paired end) to ref genome using bowtie. 2) Convert SAM file to sorted BAM file using samtools. 3) Use MACS2 to call peaks. This was done on Gal…

DiffBind macs2 chipseq

updated 7 months ago • yvonneh

Suppose that I have three conditions to compare in DiffBind, with two replicates per condition. Suppose that the antibody is the same, but one is WT and the other two - mutations

DiffBind

updated 2.7 years ago • Sam

and/or lost in each sample (enhancers created or repressed by each TF). How might I set this up in DiffBind?    Right now I have made my samples object like this: 8 Samples, 30757 sites in matrix:         &nbsp

diffbind chip-seq

updated 8.3 years ago • sarah.blackstone7734

nbsp;Hello everyone, I am having problems running diffbind count function. I keep getting the following error (running in R on Mac): <pre> > H3K9me3 = dba.count(H3K9me3, minOverlap

diffbind

updated 9.2 years ago • tassa.saldi

Hello, I am currently running an analysis using DiffBind on Cut&Run data to identify differentially expressed sites. On several occasions, after running DiffBind with...any significantly differentially bound sites? Below is the output of my command session running DiffBind: ``` > library(DiffBind) LTxding required package: GenomicRanges LTxding required package: stats4 …

Cut&Run DiffBind

updated 2.4 years ago • gannoncottone

Dear all, and Rory, I would very much appreciate if you could please advise how I shall start the DiffBind workflows from a file with peak counts (binding matrix) as an input into DiffBind. The described workflow in the vignette

DESeq2 edgeR DiffBind

updated 2.1 years ago • Bogdan

p style="direction: ltr;">Hi,</p> <p style="direction: ltr;">I have been using diffBind to analyze chip-seq data. From what I understand, diffBind creates a consensus peakset from all of the peaks given...as input. I have the diffBind report which gives me the differentially bound regions but I would like to see the consensus peakset that diffBind

diffbind peakset

updated 9.0 years ago • eli7javasky

genome separately. And now I am trying to get normalization factors for each replicate using DiffBind (v. 3.8.3), which I would like to use for differential peak analysis as well as scaling bigwig files. *Qn1:* From what I can...gather, in DiffBind, by including the spikein bam filles in the Spikein column of sampleSheet, I have the option to use the spikein library...spike-in peaks is the corre…

DiffBind SpikeIn Normalization ChIP-seq csaw

updated 23 months ago • spg

Hi everyone. I'm new at Diffbind. I'm trying to analyze my data but I noticed that if I try to run the analysis more times on the same data, the results...Hi everyone. I'm new at Diffbind. I'm trying to analyze my data but I noticed that if I try to run the analysis more times on the same data, the results change

software error DiffBind

updated 4.7 years ago • francesca3

First thing first: thanks a lot for providing the community with such a useful ChIP-seq tool as DiffBind :) It seems I am missing something in how the score column values are computed in the 1st step of reading in the datasets

diffbind score

updated 7.9 years ago • atisou

div class="preformatted">Dear All, I am using package DiffBind, Due to the fact that I miss real biological or technical replicates, I am assesing the overlapping rates between...2 Replicates, for a total of 12 Conditions > rm(list=ls()) > setwd("/home/pkunderf/output/DiffBind/ES-CMN-CMA/") > test=dba(sampleSheet="database.csv") > test 24 Samples, 19380 sites in ma…

CMA DiffBind CMA DiffBind

updated 12.3 years ago • Paolo Kunderfranco

I'm getting an error repeatable error when I try to run code that worked with previous versions of DiffBind (3.4.11) ```r meta <- read_csv("../01b_ChIPQC/HCA_chipqc_meta_final.csv")[c(3:8),] config <- data.frame(minQCth=30, fragmentSize...Traceback returns the dba() function call. This issue is resolved when I revert to R 4.1.2 and DiffBind 3.4.11. Has anyone else encountered this …

DiffBind ChIPQC

updated 2.2 years ago • ryleehackley

Dear all, I have an issue generating consensus peaks using the DiffBind package. I generate consensus peaks using the dba.peakset() function dbaObj <-  dba(sampleSheet = "samples.csv...nbsp; methods   base      other attached packages:  \[1\] DiffBind\_1.12.1     &…

chipseq diffbind

updated 10.0 years ago • Georg Otto

Hi, I have run DiffBind where the input is 200bp regions centred upon MACS2 summits run using --call-summits. I opted to run dba.count with...Hi, I have run DiffBind where the input is 200bp regions centred upon MACS2 summits run using --call-summits. I opted to run dba.count with summits=FALSE. ```r samples_qval <- dba(sampleSheet="sample_sheet_qval.csv") samples_qval <- dba.co…

DiffBind

updated 2.9 years ago • Ian

Hi, Dr Stark I find it seems that Parallel execution do not work in DiffBind when working under Windows system ``` library(DiffBind) library(BiocParallel) > tamoxifen <- dba(sampleSheet="tamoxifen.csv

DiffBind

updated 3.8 years ago • shangguandong1996

Hello, Please Ignore the below error. I found the problem. The sample table had "raw" under the PeakCaller column, as in the example, but should be "bed". ====================================== Hello, I am trying to read data into DiffBind, and I am getting an error. My sample file:   <table border="0" cellpadding="0" cellspacing="0" style="width:752px"> <tbody&g…

diffbind

updated 8.8 years ago • GFM

Hello, I have a problem with Diffbind. After the command: ``` DB_greylist <- dba.blacklist(DB, greylist=T ) ``` I get the following error: ``` Error in mclapply(seq_len

DiffBind

updated 3.9 years ago • GM

In the process of analyzing ChIP-Seq replicates with DiffBind (drosophila data, 3 replicates for each sample, choosing DESeq2 as the analysis method), peaks with very small Fold...There are no non-significant peaks above a certain, small threshold. Note: The values DiffBind returns, and are plotted, are shrunk fold changes. ---------------------- More on the data: The median absolute …

DESeq2 DiffBind

updated 3.9 years ago • Sam

I was wondering if it's possible to account for multiple factors when analyzing samples in DiffBind. I want to block for potential batch effects as well as treatment conditions, but I'm unsure how to do so (or if it's even

diffbind differential binding analysis multiple factor design

updated 4.1 years ago • jared.andrews07

peaks for my samples. For the next step I would like to perform differential peak analysis using Diffbind. But my question is how to normalize the samples using pre-calculated normalizing factor? In the Reference Manual

DiffBind

updated 3.6 years ago • mwong043

<div class="preformatted">Hello Doron- Yes, the memory usage when calling dba.count is definitely an issue one we are planning on addressing in the next version. I'll let you know what that is available. I see you are running dba.count with bParallel=FALSE, so you should only be reading in one file at a time. How large (in Gb, or how many reads) is your largest bam file? I've never seen…

DiffBind DiffBind

updated 11.8 years ago • Rory Stark

Hi, I'm trying to extract the consensus peakset that DiffBind constructs, with the raw counts in these regions. I have done this two different ways: 1) After running `dba.count()`, `dba.contrast

DiffBind

updated 4.5 years ago • hasse.bossenbroek

Hi, One of the many changes brought by DiffBind version 3.0 is the possibility of setting a model design in the same way one does in DESEq2. However, when I compare...Hi, One of the many changes brought by DiffBind version 3.0 is the possibility of setting a model design in the same way one does in DESEq2. However, when I compare the results of this new approach ("design") with those of the…

DiffBind

updated 3.3 years ago • Roger

I'm running into a curious issue with DiffBind's `` plotHeatmap `` function when used with a single contrast. It appears to either be omitting some of the results or...I'm running into a curious issue with DiffBind's `` plotHeatmap `` function when used with a single contrast. It appears to either be omitting some of the results or I

diffbind heatmap.3

updated 7.0 years ago • jared.andrews07

I may have to rephrase my question: Beyond visualization, I wanted to know if it is possible for DiffBind to identify differential peaks across all 4 different conditions. Currently, when we set a `` dba.contrast() ``, it only...nbsp; ___Original Question and Response:___ _Dear Rory,_ _I am a beginner to bioinformatics and DiffBind. Firstly, thank you for this very useful tool and the…

diffbind chipseq

updated 6.6 years ago • Shamaine

Hello, I am trying to use the DiffBind package for ATACseq analysis. When I try to use the count() function to count peaks from bed files with reads R Studio

diffbind

updated 4.5 years ago • eb19

Greetings, I am using DiffBind for a differential chromatin accessibility analysis. During manipulation of the output DARs, I noticed an inconsistency

diffbind dba.report filtering

updated 7.0 years ago • konstantopoulos

Hello, I am currently using DiffBind to analyze ATAC-seq data. I noticed that when I called `DESeq2::results` to analyze the DESeq2 object retrieved from...different number of DB sites from `dba.report` using `th = 0.05, fold = log2(1.3) `. I figured that DiffBind did ad hoc filtering in which the `fold` parameter was only used to filter peaks after the `DESeq2::results` using `alpha

DiffBind

updated 3.3 years ago • Shuwan

  Hi, I am trying to carry out some differential peak analysis on histone modification data (H3K27Ac data).  I run into problems where one peak in particular is not being called as differentially expressed, where clearly in the data is should be. In order to try and find out where the problem is I am trying to extract a bed file of the consensus peaks to make sure diffbind is…

diffbind r chipseq

updated 7.2 years ago • reubenmcgregor88

div class="preformatted">Dear All, I come back to DiffBind and tried the new version, I am analyzing some 5hmc and mc Seq experiments in a HPC server. I have both biological replicates

DiffBind DiffBind

updated 11.6 years ago • Paolo Kunderfranco

Hi, I ran DiffBind dba.blacklist function to get greylist. Then I noticed that DiffBind returns different grey lists every time I...If there is a hint to solve this problem, please let me know. Thank you. ``` >library("DiffBind") >set.seed(42) >library(BiocParallel) >register(SerialParam()) >ATAC = dba(sampleSheet="path_to_samplesheet

DiffBind

updated 14 months ago • r.murakami

two groups, and I hope to contrast them to determine differentially methylated regions/genes with DiffBind. The problem lies with the fact that I'm unsure how the data was normalized, if it was at all. Therefore, I would like to

DiffBind

updated 20 months ago • ssankar3

Hi, I have tried to run R package- DiffBind in SSH (Linux). I have R script works will with windows R 3.3.3 but failed at SSH sever linux R. It stops at dba.count step...you.  <code>#!/usr/bin/env Rscript<br/> args = commandArgs(trailingOnly=TRUE)<br/> library(DiffBind)<br/> setwd("/net/wonderland/home/zhaolinz/practice/batch8_macs2")<br/> #list.files()…

SSH atac-seq

updated 7.6 years ago • zhaolin20042008

Dear author, I am using your package Diffbind to perform chip-seq analysis of my data. In my analysis, I used three different peak callers for each sample, and I used...Dear author, I am using your package Diffbind to perform chip-seq analysis of my data. In my analysis, I used three different peak callers for each sample, and I used Diffbind to retrieve the consensus. Now, I would like to cent…

diffbind consensus

updated 7.9 years ago • pabla86

Please,     I have tried the tutorial of diffbind after installing and re-stalling the Rstudio, bioconductor and diffbind...but the dba function doesn´t go...it always

software error diffbind dba

updated 8.1 years ago • mmarins

I was trying to use Diffbind package and could not move beyond three steps.  I can see that dba object is created but without any metadata...I was trying to use Diffbind package and could not move beyond three steps.  I can see that dba object is created but without any metadata. I think that is what causing problem. Thanks for any help. Bony  __&am…

diffbind

updated 9.2 years ago • bdk

and counting from the consensus set.   Is there a way to do this using either ChIPQC or DiffBind? I really like these two packages and will definitely use them for downstream analyses on the same samples, so thought

DiffBind ChIPQC

updated 8.8 years ago • JD

Hi there, I am currently using DiffBind 3.2.7 for an analysis on RNA Polymerase III (RNAPIII) occupancy in the human genome. Because of the biology of RNAPIII

ChIPSeq DiffBind

updated 2.6 years ago • Drew

Hi,   I'd like to use Diffbind on Atac data. However what is done about the adapter adjustment that occurs before peak calling? For peak calling

Diffbind Atac adapters

updated 7.7 years ago • YaGalbi

Hi I was trying to use DiffBind to analysis my ChIP-seq data. Following the sample given by Vignette, I created my sample sheet ("my\_samples\_sheet.csv

diffbind

updated 7.8 years ago • JunLVI

Hi all, I am performing the package diffbind and at the end I would like to make two separate files for the regions that are open and closed (I am analyzing ATAC...Hi all, I am performing the package diffbind and at the end I would like to make two separate files for the regions that are open and closed (I am analyzing ATAC seq

DiffBind

updated 3.7 years ago • fleur_p90