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ChIPseq
•
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0
votes
0
replies
105
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
23 days ago
jared.andrews07
▴ 30
1
vote
1
reply
251
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 10 weeks ago by
James W. MacDonald
64k • written 10 weeks ago by
lin.pei26
• 0
0
votes
0
replies
139
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno
ChIPSeq
MotifDiscovery
10 weeks ago
franciscrick41
• 0
2
votes
14
replies
771
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno
ChIPSeq
updated 3 months ago by
James W. MacDonald
64k • written 3 months ago by
Jerina
▴ 10
0
votes
5
replies
1.3k
views
diffbind
DiffBind
chipseq
updated 4 months ago by
Rory Stark
★ 5.1k • written 4 months ago by
ANAMIKA
• 0
1
vote
4
replies
658
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 6 months ago by
Rory Stark
★ 5.1k • written 6 months ago by
lin.pei26
• 0
0
votes
2
replies
429
views
annotate peaks using a custom genome
ChIPSeq
annotate
ChIPpeakAnno
updated 7 months ago by
Kai Hu
▴ 70 • written 7 months ago by
C T
▴ 140
5
votes
8
replies
742
views
Help with error install csaw
ChIPSeq
ATACSeq
updated 8 months ago by
nekisaf309
• 0 • written 8 months ago by
Chris
• 0
0
votes
2
replies
740
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
8 months ago
Giulia
• 0
0
votes
0
replies
302
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
8 months ago
Giulia
• 0
1
vote
2
replies
700
views
how i can get the name of genes in pathway?
chipseq
ChIPseeker
9 months ago
chavaleab
• 0
1
vote
3
replies
484
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
9 months ago
stacy.genovese
• 0
1
vote
4
replies
842
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq
PeakDetection
11 months ago • updated 10 months ago
stacy.genovese
• 0
0
votes
2
replies
578
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq
ChIPSeqData
chipseqDB
12 months ago
stacy.genovese
• 0
0
votes
1
reply
705
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq
DiffBind
updated 14 months ago by
Rory Stark
★ 5.1k • written 14 months ago by
Nicole
• 0
6
votes
3
replies
1.1k
views
MEDIPS for chIP-Seq
ChIPSeq
written 16 months ago by
Darek
▴ 30
0
votes
7
replies
1.5k
views
CHIPQC error regarding BiocParallel
CHIPQC
Diffbind
chipseq
rory stark
Thomas Carroll
updated 16 months ago by
arisarkar88
▴ 40 • written 3.6 years ago by
bioinfouser2
▴ 10
0
votes
1
reply
726
views
Job:
'Omics data analyst for HPCBio, University of Illinois
Metagenomics
GenomicVariation
Genomics
RNASeq
ChIPSeq
16 months ago
Jenny Drnevich
★ 2.0k
0
votes
0
replies
546
views
intron coordination and annotation
ChIPSeq
updated 16 months ago by
ATpoint
★ 3.6k • written 17 months ago by
mehdi
• 0
0
votes
0
replies
641
views
Job:
Bioinformatics Research Scientist- Epigenetics Group
HiC
Epigenetics
HiCHIP
ChIPSeq
18 months ago
xubeisi
• 0
0
votes
1
reply
584
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno
ChIPSeq
updated 19 months ago by
Ou, Jianhong
★ 1.3k • written 19 months ago by
Abhilansh
• 0
0
votes
3
replies
825
views
DiffBind on static peak set for all samples
ChIPSeq
DiffBind
updated 19 months ago by
Rory Stark
★ 5.1k • written 19 months ago by
Drew
• 0
0
votes
0
replies
560
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq
ChIPseeker
19 months ago
Swadha
• 0
0
votes
1
reply
697
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq
DiffBind
updated 20 months ago by
Rory Stark
★ 5.1k • written 21 months ago by
rita.rebollo
• 0
1
vote
2
replies
1.0k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 21 months ago by
Rory Stark
★ 5.1k • written 21 months ago by
maria.soler
• 0
1
vote
1
reply
837
views
DiffBind scoreCol value question
DiffBind
ChIPSeq
chipseq
updated 23 months ago by
Rory Stark
★ 5.1k • written 24 months ago by
erbrocato
• 0
0
votes
0
replies
632
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks
ChIPpeakAnno
chipseq
2.0 years ago
Nadav
• 0
0
votes
0
replies
795
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind
ChIPSeq
Normalization
SpikeIn
2.2 years ago
Drew
• 0
0
votes
6
replies
1.4k
views
cel files with affy library
ChIPSeq
updated 2.3 years ago by
almaza24map
• 0 • written 2.3 years ago by
scipio04
• 0
3
votes
12
replies
2.8k
views
Is it possible to change how DiffBind merge peaks?
DiffBind
ChIPseq
updated 2.3 years ago by
Rory Stark
★ 5.1k • written 4.2 years ago by
zhenfeng.liu1
▴ 20
0
votes
2
replies
961
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq
SpikeIn
edgeR
Normalization
2.4 years ago • updated 2.3 years ago
maria.soler
• 0
2
votes
3
replies
1.1k
views
An error using Diffbind plotprofile
ChIPSeq
profileplyr
DiffBind
updated 2.3 years ago by
doug.barrows
▴ 20 • written 2.4 years ago by
zhuyi05
• 0
5
votes
8
replies
1.9k
views
how to construct a DBA object from count matrix
ChIPSeq
ATACSeq
differentially_occupied
DiffBind
updated 18 months ago by
Johanna Hardin
▴ 20 • written 2.4 years ago by
pegah.taklifi
▴ 30
0
votes
1
reply
1.6k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq
SICER2
DiffBind
MACS2
offtopic
updated 2.5 years ago by
James W. MacDonald
64k • written 2.5 years ago by
Yuan Tian
▴ 270
2
votes
5
replies
2.7k
views
News:
New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr
ATACSeq
DiffBind
ComplexHeatmap
ChIPSeq
updated 12 months ago by
Junsik
• 0 • written 2.5 years ago by
Rory Stark
★ 5.1k
2
votes
4
replies
1.1k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq
csaw;
crosscorrelation
2.6 years ago • updated 2.5 years ago
richardallenfriedmanbrooklyn
• 0
0
votes
0
replies
1.5k
views
Blacklist error at dba.analyze(dbObj)
DiffBind
ChIPSeq
2.7 years ago
Goku
• 0
2
votes
6
replies
1.2k
views
Error with dba.count(dbObj) in DiffBind
DiffBind
ChIPSeq
2.7 years ago
Goku
• 0
0
votes
3
replies
890
views
Which library now contains the ssdCoverage command that used to be found in the htseqtools package for R version 4.0.1 ?
Deprecation
chipseq
htseqtools
Bioconductor
updated 2.7 years ago by
Basti
▴ 740 • written 2.8 years ago by
Mick
• 0
1
vote
4
replies
1.1k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq
DiffBind
ExperimentalDesign
2.8 years ago
SFn
• 0
0
votes
11
replies
1.7k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq
ChIPSeqSpike
updated 2.8 years ago by
nicolas.descostes
• 0 • written 2.9 years ago by
Ainul
• 0
0
votes
2
replies
928
views
DiffBind Error When using dba.count()
ChIP-Rx
DiffBind
chipseq
3.0 years ago
indi97
• 0
2
votes
2
replies
2.2k
views
ChIP seeker annotation error
DiffBind
chipseq
ChIPseeker
ChipDb
annotation
3.1 years ago • updated 2.8 years ago
Mar Mar
▴ 20
1
vote
4
replies
1.8k
views
MAnorm output as DiffBind input.
MAnorm
diffbind
normalization
chipseq
updated 3.1 years ago by
Rory Stark
★ 5.1k • written 5.9 years ago by
ajeet
• 0
2
votes
4
replies
1.6k
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind
Chipseq
spike-ins
updated 3.1 years ago by
Rory Stark
★ 5.1k • written 4.1 years ago by
Konstantin Okonechnikov
▴ 40
4
votes
3
replies
846
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind
block
regression
deseq2
chipseq
updated 3.1 years ago by
Rory Stark
★ 5.1k • written 4.1 years ago by
melnuesch
▴ 10
1
vote
3
replies
2.5k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind
chipseq
chipqc
updated 3.1 years ago by
Rory Stark
★ 5.1k • written 5.8 years ago by
bioinfouser2
▴ 10
1
vote
9
replies
2.5k
views
Spike-in normalization in EdgeR
CUTandRUN
edgeR
Normalization
SpikeIn
ChIPSeq
updated 12 months ago by
Bogdan
▴ 670 • written 3.1 years ago by
Hesh
▴ 10
1
vote
1
reply
1.4k
views
News:
Extensive updates in DiffBind 3.0
Normalization
ATACSeq
ChIPSeq
DiffBind
chipseq
written 3.1 years ago by
Rory Stark
★ 5.1k
0
votes
1
reply
1.2k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR
ChIPs
ChIPseeker
ChIPSeq
chipseq
updated 3.1 years ago by
James W. MacDonald
64k • written 3.1 years ago by
ret28
• 0
50 results • Page
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Comment: Correct the batch effect in methylation analysis in R
by
kyj2226
• 0
Thank you for your response Gordon :) I've already run the code below, just add batch to the limma linear model design <- model.matri…
Answer: Correct the batch effect in methylation analysis in R
by
Gordon Smyth
49k
You should not apply batch correction functions like harman before a limma analysis. Instead, just add `batch` to the limma linear model. …
Answer: Agilent Microarray Gene Oncology analysis gone wrong
by
Gordon Smyth
49k
Your use of `coef=1` is incorrect, for reasons explained in the limma User's Guide. If you had simply left `coef` at the default, then thin…
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by
Shaimaa Gamal
• 0
Hello I was wondering if I should use ruv-corrected counts and ruv lib sizes to create a DGE object that can be used later for DE analysis …
Comment: enrichGOgradient color change
by
James W. MacDonald
64k
You could look at my answer and extrapolate from there.
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Answer: Correct the batch effect in methylation analysis in R
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Answer: Filter genes by expression for voomLmFit
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