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
Order by: Relevance
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
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
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
updated 8.7 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
updated 4.6 years ago • fleur_p90
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
updated 19 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…
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…
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…
updated 22 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
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
updated 4.4 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
updated 3.9 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…
updated 15 months ago • jesswhitts
hi Rory,
I'm a new with DiffBind for d<span style="background-color:rgba(0, 0, 0, 0)">i fferential binding analysis of ChIP-Seq peak
updated 10.1 years ago • February
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…
updated 10.5 years ago • Nicolas Delhomme
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
updated 3.4 years ago • ipsc-jl
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!
 
updated 7.9 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
updated 4.5 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"…
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
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
Hi,
Recently I'm using DiffBind.
After running dba.count, I can use tamoxifen$binding to get a table.
> head(tamoxifen$binding)
CHR  ...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 &…
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
updated 10.9 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
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…
updated 3.4 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
updated 3.6 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…
narrow```
Here is the code for DiffBind Analysis
```r
library(DiffBind)
treg=dba(sampleSheet="PS_Treg_atacseq-1.csv")
treg=dba.count(treg,bUseSummarizeOverlaps
nbsp;methods
\[9\] base
other attached packages:
\[1\] DiffBind\_1.16.3 RSQLite\_1.0.0 DBI\_0.3.1  
updated 9.7 years ago • Udi Landau
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
updated 3.7 years ago • r.finn
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
updated 4.9 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…
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
updated 9.2 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
updated 4.3 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 …
updated 16 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
updated 4.2 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
updated 4.3 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
updated 6.0 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
updated 5.1 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
updated 12.2 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
updated 10.5 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
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
updated 10.5 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
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
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
updated 10.5 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
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…
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
updated 4.3 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
updated 4.9 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",
…
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
updated 5.0 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…
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
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…
updated 8.5 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
To preface this,
I have used DiffBind and csaw for most of my experimental work and love these programs, this is just a general question I had and I have...To preface this,
I have used DiffBind and csaw for most of my experimental work and love these programs, this is just a general question I had and I have seen versions of these questions asked before on this forum - but would like to ask…
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
updated 5.3 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
updated 4.8 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
Recent ...
Replies
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts
by
Michael Love
43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts
by
empty_mt
•
0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something?
I have 6 treatments, …
Comment: deseq2 filter the low counts
by
Michael Love
43k
Have you seen this part:
https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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