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Showing :
chipseq
•
reset
0
votes
0
replies
88
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
14 days ago
yvonneh
• 0
0
votes
1
reply
133
views
what is the sampleFiles
chipseq
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
zhulin
• 0
0
votes
0
replies
190
views
Best method for annotating distal peaks
ChIPSeq
annotation
ChIPpeakAnno
3 months ago
nilanjanamani88
• 0
1
vote
3
replies
425
views
Big differences between biological replicates makes DESeq2 result 0
chipseq
DifferentialMethylation
DESeq2
updated 3 months ago by
Michael Love
42k • written 3 months ago by
rebw25
• 0
0
votes
0
replies
187
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
3 months ago
frueher
• 0
0
votes
0
replies
347
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
6 months ago
jared.andrews07
▴ 30
1
vote
1
reply
469
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
lin.pei26
• 0
0
votes
0
replies
295
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno
ChIPSeq
MotifDiscovery
7 months ago
franciscrick41
• 0
2
votes
14
replies
1.2k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno
ChIPSeq
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
Jerina
▴ 10
0
votes
5
replies
3.2k
views
diffbind
DiffBind
chipseq
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
ANAMIKA
• 0
1
vote
4
replies
1.0k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 11 months ago by
Rory Stark
★ 5.2k • written 11 months ago by
lin.pei26
• 0
0
votes
2
replies
624
views
annotate peaks using a custom genome
ChIPSeq
annotate
ChIPpeakAnno
updated 12 months ago by
Kai Hu
▴ 70 • written 13 months ago by
C T
▴ 140
5
votes
8
replies
1.1k
views
Help with error install csaw
ChIPSeq
ATACSeq
written 13 months ago by
Chris
▴ 10
0
votes
2
replies
1.1k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
14 months ago • updated 13 months ago
Giulia
• 0
0
votes
0
replies
458
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
13 months ago
Giulia
• 0
1
vote
2
replies
1.1k
views
how i can get the name of genes in pathway?
chipseq
ChIPseeker
14 months ago
chavaleab
• 0
1
vote
3
replies
709
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
15 months ago
stacy.genovese
• 0
1
vote
4
replies
1.2k
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq
PeakDetection
16 months ago
stacy.genovese
• 0
0
votes
2
replies
791
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq
ChIPSeqData
chipseqDB
17 months ago
stacy.genovese
• 0
0
votes
1
reply
882
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq
DiffBind
updated 19 months ago by
Rory Stark
★ 5.2k • written 19 months ago by
Nicole
• 0
6
votes
3
replies
1.4k
views
MEDIPS for chIP-Seq
ChIPSeq
written 21 months ago by
Darek
▴ 30
0
votes
7
replies
1.9k
views
CHIPQC error regarding BiocParallel
CHIPQC
Diffbind
chipseq
rory stark
Thomas Carroll
updated 21 months ago by
arisarkar88
▴ 40 • written 4.1 years ago by
bioinfouser2
▴ 10
0
votes
1
reply
913
views
Job:
'Omics data analyst for HPCBio, University of Illinois
Metagenomics
GenomicVariation
Genomics
RNASeq
ChIPSeq
22 months ago • updated 21 months ago
Jenny Drnevich
★ 2.0k
0
votes
0
replies
706
views
intron coordination and annotation
ChIPSeq
updated 22 months ago by
ATpoint
★ 4.1k • written 22 months ago by
mehdi
• 0
0
votes
0
replies
819
views
Job:
Bioinformatics Research Scientist- Epigenetics Group
HiC
Epigenetics
HiCHIP
ChIPSeq
23 months ago
xubeisi
• 0
0
votes
1
reply
719
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno
ChIPSeq
updated 2.0 years ago by
Ou, Jianhong
★ 1.3k • written 2.0 years ago by
Abhilansh
• 0
0
votes
3
replies
1.0k
views
DiffBind on static peak set for all samples
ChIPSeq
DiffBind
updated 2.0 years ago by
Rory Stark
★ 5.2k • written 2.0 years ago by
Drew
• 0
0
votes
0
replies
701
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq
ChIPseeker
2.1 years ago
Swadha
• 0
0
votes
1
reply
878
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq
DiffBind
updated 2.1 years ago by
Rory Stark
★ 5.2k • written 2.2 years ago by
rita.rebollo
• 0
1
vote
2
replies
1.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 2.2 years ago by
Rory Stark
★ 5.2k • written 2.2 years ago by
maria.soler
• 0
1
vote
1
reply
1.0k
views
DiffBind scoreCol value question
DiffBind
ChIPSeq
chipseq
updated 2.4 years ago by
Rory Stark
★ 5.2k • written 2.4 years ago by
erbrocato
• 0
0
votes
0
replies
749
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks
ChIPpeakAnno
chipseq
2.4 years ago
Nadav
• 0
0
votes
0
replies
913
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind
ChIPSeq
Normalization
SpikeIn
2.6 years ago
Drew
• 0
0
votes
6
replies
1.7k
views
cel files with affy library
ChIPSeq
updated 2.8 years ago by
almaza24map
• 0 • written 2.8 years ago by
scipio04
• 0
3
votes
12
replies
3.4k
views
Is it possible to change how DiffBind merge peaks?
DiffBind
ChIPseq
updated 2.8 years ago by
Rory Stark
★ 5.2k • written 4.7 years ago by
zhenfeng.liu1
▴ 20
0
votes
2
replies
1.1k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq
SpikeIn
edgeR
Normalization
2.8 years ago
maria.soler
• 0
2
votes
3
replies
1.4k
views
An error using Diffbind plotprofile
ChIPSeq
profileplyr
DiffBind
updated 2.7 years ago by
doug.barrows
▴ 20 • written 2.8 years ago by
zhuyi05
• 0
5
votes
8
replies
2.2k
views
how to construct a DBA object from count matrix
ChIPSeq
ATACSeq
differentially_occupied
DiffBind
updated 23 months ago by
Johanna Hardin
▴ 20 • written 2.8 years ago by
pegah.taklifi
▴ 30
0
votes
1
reply
1.8k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq
SICER2
DiffBind
MACS2
offtopic
updated 3.0 years ago by
James W. MacDonald
65k • written 3.0 years ago by
Yuan Tian
▴ 290
2
votes
5
replies
3.4k
views
News:
New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr
ATACSeq
DiffBind
ComplexHeatmap
ChIPSeq
updated 17 months ago by
Junsik
• 0 • written 3.0 years ago by
Rory Stark
★ 5.2k
2
votes
4
replies
1.2k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq
csaw;
crosscorrelation
3.0 years ago
richardallenfriedmanbrooklyn
▴ 20
0
votes
0
replies
1.7k
views
Blacklist error at dba.analyze(dbObj)
DiffBind
ChIPSeq
3.1 years ago
Goku
• 0
2
votes
6
replies
1.5k
views
Error with dba.count(dbObj) in DiffBind
DiffBind
ChIPSeq
3.2 years ago • updated 3.1 years ago
Goku
• 0
0
votes
3
replies
1.0k
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 3.2 years ago by
Basti
▴ 780 • written 3.2 years ago by
Mick
• 0
1
vote
4
replies
1.4k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq
DiffBind
ExperimentalDesign
3.3 years ago • updated 3.2 years ago
SFn
• 0
0
votes
11
replies
2.0k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq
ChIPSeqSpike
updated 3.3 years ago by
nicolas.descostes
• 0 • written 3.3 years ago by
Ainul
• 0
0
votes
2
replies
1.1k
views
DiffBind Error When using dba.count()
ChIP-Rx
DiffBind
chipseq
3.5 years ago • updated 3.4 years ago
indi97
• 0
2
votes
2
replies
2.4k
views
ChIP seeker annotation error
DiffBind
chipseq
ChIPseeker
ChipDb
annotation
3.5 years ago • updated 3.3 years ago
Mar Mar
▴ 20
1
vote
4
replies
2.0k
views
MAnorm output as DiffBind input.
MAnorm
diffbind
normalization
chipseq
updated 3.5 years ago by
Rory Stark
★ 5.2k • written 6.3 years ago by
ajeet
• 0
2
votes
4
replies
1.8k
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind
Chipseq
spike-ins
updated 3.5 years ago by
Rory Stark
★ 5.2k • written 4.5 years ago by
Konstantin Okonechnikov
▴ 40
50 results • Page
1 of 1
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Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
makala
• 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
Erik Wright
▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
by
Matthew Thornton
▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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