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chipseq
•
reset
0
votes
0
replies
126
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
14 days ago
atlanta
• 0
0
votes
0
replies
83
views
News:
Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq
MNaseSeq
ATACSeq
22 days ago • updated 18 days ago
info
▴ 10
1
vote
8
replies
2.3k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
6 weeks ago • updated 15 days ago
Luca
• 0
1
vote
3
replies
783
views
Csaw normalization strategies - general inquiry
ChIPSeq
csaw
updated 12 weeks ago by
franknappi14
• 0 • written 3 months ago by
Luca
• 0
6
votes
5
replies
2.0k
views
MEDIPS for chIP-Seq
ChIPSeq
written 2.7 years ago by
Darek
▴ 30
0
votes
0
replies
219
views
ChIP peaks comparison
ChIPSeqData
genomes
ChIPSeq
5 months ago
user_bioinfo
• 0
0
votes
0
replies
319
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
7 months ago
Alejandro
• 0
0
votes
0
replies
514
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
10 months ago
gamma.jian
▴ 10
0
votes
0
replies
519
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
11 months ago
yvonneh
• 0
0
votes
1
reply
401
views
what is the sampleFiles
chipseq
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
zhulin
• 0
0
votes
0
replies
624
views
Best method for annotating distal peaks
ChIPSeq
annotation
ChIPpeakAnno
14 months ago
nilanjanamani88
• 0
1
vote
3
replies
879
views
Big differences between biological replicates makes DESeq2 result 0
chipseq
DifferentialMethylation
DESeq2
updated 14 months ago by
Michael Love
43k • written 15 months ago by
rebw25
• 0
0
votes
0
replies
455
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
15 months ago
frueher
• 0
0
votes
0
replies
767
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
17 months ago
jared.andrews07
▴ 30
1
vote
1
reply
966
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
lin.pei26
• 0
0
votes
0
replies
579
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno
ChIPSeq
MotifDiscovery
19 months ago
franciscrick41
• 0
2
votes
14
replies
2.0k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno
ChIPSeq
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Jerina
▴ 10
0
votes
5
replies
7.2k
views
diffbind
DiffBind
chipseq
updated 21 months ago by
Rory Stark
★ 5.2k • written 21 months ago by
ANAMIKA
• 0
1
vote
4
replies
2.0k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 23 months ago by
Rory Stark
★ 5.2k • written 23 months ago by
lin.pei26
• 0
0
votes
2
replies
1.1k
views
annotate peaks using a custom genome
ChIPSeq
annotate
ChIPpeakAnno
updated 24 months ago by
Kai Hu
▴ 70 • written 2.0 years ago by
C T
▴ 140
5
votes
8
replies
1.6k
views
Help with error install csaw
ChIPSeq
ATACSeq
written 2.1 years ago by
Chris
▴ 20
0
votes
2
replies
1.8k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
2.1 years ago
Giulia
• 0
0
votes
0
replies
685
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
2.1 years ago
Giulia
• 0
1
vote
2
replies
1.6k
views
how i can get the name of genes in pathway?
chipseq
ChIPseeker
2.1 years ago
chavaleab
• 0
1
vote
3
replies
1.1k
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
2.2 years ago
stacy.genovese
• 0
1
vote
4
replies
2.0k
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq
PeakDetection
2.3 years ago
stacy.genovese
• 0
0
votes
2
replies
1.2k
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq
ChIPSeqData
chipseqDB
2.4 years ago
stacy.genovese
• 0
0
votes
1
reply
1.2k
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq
DiffBind
updated 2.5 years ago by
Rory Stark
★ 5.2k • written 2.5 years ago by
Nicole
• 0
0
votes
7
replies
2.5k
views
CHIPQC error regarding BiocParallel
CHIPQC
Diffbind
chipseq
rory stark
Thomas Carroll
updated 2.7 years ago by
arisarkar88
▴ 40 • written 5.0 years ago by
bioinfouser2
▴ 10
0
votes
1
reply
1.2k
views
Job:
'Omics data analyst for HPCBio, University of Illinois
Metagenomics
GenomicVariation
Genomics
RNASeq
ChIPSeq
2.8 years ago • updated 2.7 years ago
Jenny Drnevich
★ 2.0k
0
votes
0
replies
1.1k
views
intron coordination and annotation
ChIPSeq
updated 2.8 years ago by
ATpoint
★ 4.8k • written 2.8 years ago by
mehdi
• 0
0
votes
0
replies
1.1k
views
Job:
Bioinformatics Research Scientist- Epigenetics Group
HiC
Epigenetics
HiCHIP
ChIPSeq
2.9 years ago
xubeisi
• 0
0
votes
1
reply
948
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno
ChIPSeq
updated 2.9 years ago by
Ou, Jianhong
★ 1.3k • written 2.9 years ago by
Abhilansh
• 0
0
votes
3
replies
1.5k
views
DiffBind on static peak set for all samples
ChIPSeq
DiffBind
updated 3.0 years ago by
Rory Stark
★ 5.2k • written 3.0 years ago by
Drew
• 0
0
votes
0
replies
962
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq
ChIPseeker
3.0 years ago
Swadha
• 0
0
votes
1
reply
1.2k
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq
DiffBind
updated 3.1 years ago by
Rory Stark
★ 5.2k • written 3.1 years ago by
rita.rebollo
• 0
1
vote
2
replies
1.9k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 3.1 years ago by
Rory Stark
★ 5.2k • written 3.1 years ago by
maria.soler
• 0
1
vote
1
reply
1.4k
views
DiffBind scoreCol value question
DiffBind
ChIPSeq
chipseq
updated 3.3 years ago by
Rory Stark
★ 5.2k • written 3.4 years ago by
erbrocato
• 0
0
votes
0
replies
1.0k
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks
ChIPpeakAnno
chipseq
3.4 years ago
Nadav
• 0
0
votes
0
replies
1.2k
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind
ChIPSeq
Normalization
SpikeIn
3.6 years ago
Drew
• 0
0
votes
6
replies
2.6k
views
cel files with affy library
ChIPSeq
updated 3.7 years ago by
almaza24map
• 0 • written 3.7 years ago by
scipio04
• 0
3
votes
12
replies
4.7k
views
Is it possible to change how DiffBind merge peaks?
DiffBind
ChIPseq
updated 3.7 years ago by
Rory Stark
★ 5.2k • written 5.6 years ago by
zhenfeng.liu1
▴ 20
0
votes
2
replies
1.6k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq
SpikeIn
edgeR
Normalization
3.7 years ago
maria.soler
• 0
2
votes
3
replies
2.0k
views
An error using Diffbind plotprofile
ChIPSeq
profileplyr
DiffBind
updated 3.6 years ago by
doug.barrows
▴ 20 • written 3.7 years ago by
zhuyi05
• 0
5
votes
8
replies
2.9k
views
how to construct a DBA object from count matrix
ChIPSeq
ATACSeq
differentially_occupied
DiffBind
updated 2.9 years ago by
Johanna Hardin
▴ 20 • written 3.8 years ago by
pegah.taklifi
▴ 30
0
votes
1
reply
2.4k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq
SICER2
DiffBind
MACS2
offtopic
updated 3.9 years ago by
James W. MacDonald
68k • written 3.9 years ago by
Yuan Tian
▴ 290
2
votes
5
replies
5.1k
views
News:
New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr
ATACSeq
DiffBind
ComplexHeatmap
ChIPSeq
updated 2.4 years ago by
Junsik
• 0 • written 3.9 years ago by
Rory Stark
★ 5.2k
2
votes
4
replies
1.7k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq
csaw;
crosscorrelation
4.0 years ago • updated 3.9 years ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
0
replies
2.1k
views
Blacklist error at dba.analyze(dbObj)
DiffBind
ChIPSeq
4.1 years ago
Goku
• 0
2
votes
6
replies
2.0k
views
Error with dba.count(dbObj) in DiffBind
DiffBind
ChIPSeq
4.1 years ago
Goku
• 0
50 results • Page
1 of 1
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Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
donnycrimson
• 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Comment: CluserProfiler message "No gene can be mapped"
by
Carolina
• 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2
by
JKim
• 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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