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Showing :
Chipseq
•
reset
0
votes
0
replies
36
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
1 day ago
yvonneh
• 0
0
votes
1
reply
119
views
what is the sampleFiles
chipseq
updated 18 days ago by
James W. MacDonald
65k • written 18 days ago by
zhulin
• 0
0
votes
0
replies
169
views
Best method for annotating distal peaks
ChIPSeq
annotation
ChIPpeakAnno
12 weeks ago
nilanjanamani88
• 0
1
vote
3
replies
397
views
Big differences between biological replicates makes DESeq2 result 0
chipseq
DifferentialMethylation
DESeq2
updated 3 months ago by
Michael Love
41k • written 3 months ago by
rebw25
• 0
0
votes
0
replies
176
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
3 months ago
frueher
• 0
0
votes
0
replies
332
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
5 months ago
jared.andrews07
▴ 30
1
vote
1
reply
449
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
285
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
1.1k
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
3.0k
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
609
views
annotate peaks using a custom genome
ChIPSeq
annotate
ChIPpeakAnno
updated 12 months ago by
Kai Hu
▴ 70 • written 12 months ago by
C T
▴ 140
5
votes
8
replies
1.0k
views
Help with error install csaw
ChIPSeq
ATACSeq
written 13 months ago by
Chris
• 0
0
votes
0
replies
450
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
13 months ago
Giulia
• 0
0
votes
2
replies
1.1k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
13 months ago
Giulia
• 0
1
vote
2
replies
1.0k
views
how i can get the name of genes in pathway?
chipseq
ChIPseeker
14 months ago
chavaleab
• 0
1
vote
3
replies
694
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
14 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 • updated 15 months ago
stacy.genovese
• 0
0
votes
2
replies
776
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq
ChIPSeqData
chipseqDB
17 months ago
stacy.genovese
• 0
0
votes
1
reply
874
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq
DiffBind
updated 18 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
1
reply
904
views
Job:
'Omics data analyst for HPCBio, University of Illinois
Metagenomics
GenomicVariation
Genomics
RNASeq
ChIPSeq
21 months ago
Jenny Drnevich
★ 2.0k
0
votes
0
replies
696
views
intron coordination and annotation
ChIPSeq
updated 21 months ago by
ATpoint
★ 4.1k • written 21 months ago by
mehdi
• 0
0
votes
0
replies
800
views
Job:
Bioinformatics Research Scientist- Epigenetics Group
HiC
Epigenetics
HiCHIP
ChIPSeq
22 months ago
xubeisi
• 0
0
votes
1
reply
709
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno
ChIPSeq
updated 23 months ago by
Ou, Jianhong
★ 1.3k • written 23 months ago by
Abhilansh
• 0
0
votes
3
replies
1.0k
views
DiffBind on static peak set for all samples
ChIPSeq
DiffBind
updated 24 months ago by
Rory Stark
★ 5.2k • written 24 months ago by
Drew
• 0
0
votes
0
replies
692
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq
ChIPseeker
2.0 years ago
Swadha
• 0
1
vote
2
replies
1.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 2.1 years ago by
Rory Stark
★ 5.2k • written 2.1 years ago by
maria.soler
• 0
0
votes
1
reply
863
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
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
741
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks
ChIPpeakAnno
chipseq
2.4 years ago
Nadav
• 0
0
votes
0
replies
906
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 2.7 years ago by
almaza24map
• 0 • written 2.7 years ago by
scipio04
• 0
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 • updated 2.7 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 2.9 years ago by
James W. MacDonald
65k • written 2.9 years ago by
Yuan Tian
▴ 280
2
votes
5
replies
3.3k
views
News:
New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr
ATACSeq
DiffBind
ComplexHeatmap
ChIPSeq
updated 16 months ago by
Junsik
• 0 • written 2.9 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 • updated 2.9 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
3.1 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 3.1 years ago by
Basti
▴ 780 • written 3.2 years ago by
Mick
• 0
1
vote
4
replies
1.3k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq
DiffBind
ExperimentalDesign
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 3.2 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
3.4 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 3.2 years ago
Mar Mar
▴ 20
1
vote
1
reply
1.5k
views
News:
Extensive updates in DiffBind 3.0
Normalization
ATACSeq
ChIPSeq
DiffBind
chipseq
written 3.5 years ago by
Rory Stark
★ 5.2k
1
vote
9
replies
3.0k
views
Spike-in normalization in EdgeR
CUTandRUN
edgeR
Normalization
SpikeIn
ChIPSeq
updated 17 months ago by
Bogdan
▴ 670 • written 3.5 years ago by
Hesh
▴ 10
0
votes
1
reply
1.4k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR
ChIPs
ChIPseeker
ChIPSeq
chipseq
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
ret28
• 0
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 4.0 years ago by
bioinfouser2
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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