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ChIPSeq
•
reset
1
vote
4
replies
144
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq
PeakDetection
5 weeks ago • updated 22 days ago
stacy.genovese
• 0
0
votes
2
replies
163
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq
ChIPSeqData
chipseqDB
10 weeks ago
stacy.genovese
• 0
0
votes
1
reply
253
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq
DiffBind
updated 3 months ago by
Rory Stark
★ 4.6k • written 4 months ago by
Nicole
• 0
3
votes
3
replies
395
views
MEDIPS for chIP-Seq
ChIPSeq
written 6 months ago by
Darek
▴ 10
0
votes
7
replies
902
views
CHIPQC error regarding BiocParallel
CHIPQC
Diffbind
chipseq
rory stark
Thomas Carroll
updated 6 months ago by
arisarkar88
▴ 10 • written 2.8 years ago by
bioinfouser2
▴ 10
0
votes
1
reply
289
views
Job:
'Omics data analyst for HPCBio, University of Illinois
Metagenomics
GenomicVariation
Genomics
RNASeq
ChIPSeq
6 months ago
Jenny Drnevich
★ 2.0k
0
votes
0
replies
174
views
intron coordination and annotation
ChIPSeq
updated 6 months ago by
ATpoint
★ 2.1k • written 6 months ago by
mehdi
• 0
0
votes
0
replies
267
views
Job:
Bioinformatics Research Scientist- Epigenetics Group
HiC
Epigenetics
HiCHIP
ChIPSeq
7 months ago
xubeisi
• 0
0
votes
1
reply
263
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno
ChIPSeq
updated 8 months ago by
Ou, Jianhong
★ 1.3k • written 8 months ago by
Abhilansh
• 0
0
votes
3
replies
368
views
DiffBind on static peak set for all samples
ChIPSeq
DiffBind
updated 9 months ago by
Rory Stark
★ 4.6k • written 9 months ago by
Drew
• 0
0
votes
0
replies
231
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq
ChIPseeker
9 months ago
Swadha
• 0
0
votes
1
reply
356
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq
DiffBind
updated 10 months ago by
Rory Stark
★ 4.6k • written 11 months ago by
rita.rebollo
• 0
1
vote
2
replies
555
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 10 months ago by
Rory Stark
★ 4.6k • written 10 months ago by
maria.soler
• 0
1
vote
1
reply
502
views
DiffBind scoreCol value question
DiffBind
ChIPSeq
chipseq
updated 13 months ago by
Rory Stark
★ 4.6k • written 13 months ago by
erbrocato
• 0
0
votes
0
replies
345
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks
ChIPpeakAnno
chipseq
14 months ago
Nadav
• 0
0
votes
0
replies
435
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind
ChIPSeq
Normalization
SpikeIn
16 months ago
Drew
• 0
0
votes
6
replies
863
views
cel files with affy library
ChIPSeq
updated 18 months ago by
almaza24map
• 0 • written 18 months ago by
scipio04
• 0
3
votes
12
replies
1.6k
views
Is it possible to change how DiffBind merge peaks?
DiffBind
ChIPseq
updated 18 months ago by
Rory Stark
★ 4.6k • written 3.4 years ago by
zhenfeng.liu1
▴ 20
0
votes
2
replies
574
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq
SpikeIn
edgeR
Normalization
18 months ago
maria.soler
• 0
2
votes
3
replies
615
views
An error using Diffbind plotprofile
ChIPSeq
profileplyr
DiffBind
updated 17 months ago by
doug.barrows
▴ 20 • written 18 months ago by
zhuyi05
• 0
5
votes
8
replies
1.1k
views
how to construct a DBA object from count matrix
ChIPSeq
ATACSeq
differentially_occupied
DiffBind
updated 8 months ago by
Johanna Hardin
▴ 20 • written 19 months ago by
pegah.taklifi
▴ 30
0
votes
1
reply
935
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq
SICER2
DiffBind
MACS2
offtopic
updated 20 months ago by
James W. MacDonald
62k • written 20 months ago by
Yuan Tian
▴ 250
2
votes
5
replies
1.4k
views
News:
New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr
ATACSeq
DiffBind
ComplexHeatmap
ChIPSeq
updated 8 weeks ago by
Junsik
• 0 • written 20 months ago by
Rory Stark
★ 4.6k
2
votes
4
replies
652
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq
csaw;
crosscorrelation
21 months ago • updated 20 months ago
richardallenfriedmanbrooklyn
• 0
0
votes
0
replies
885
views
Blacklist error at dba.analyze(dbObj)
DiffBind
ChIPSeq
22 months ago
Goku
• 0
2
votes
6
replies
691
views
Error with dba.count(dbObj) in DiffBind
DiffBind
ChIPSeq
22 months ago
Goku
• 0
0
votes
3
replies
557
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 23 months ago by
Basti
▴ 540 • written 23 months ago by
Mick
• 0
1
vote
4
replies
666
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq
DiffBind
ExperimentalDesign
24 months ago • updated 23 months ago
SFn
• 0
0
votes
11
replies
1.1k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq
ChIPSeqSpike
updated 2.0 years ago by
nicolas.descostes
• 0 • written 2.1 years ago by
Ainul
• 0
0
votes
2
replies
554
views
DiffBind Error When using dba.count()
ChIP-Rx
DiffBind
chipseq
2.2 years ago
indi97
• 0
2
votes
2
replies
1.6k
views
ChIP seeker annotation error
DiffBind
chipseq
ChIPseeker
ChipDb
annotation
2.2 years ago • updated 2.0 years ago
Mar Mar
▴ 20
1
vote
4
replies
1.3k
views
MAnorm output as DiffBind input.
MAnorm
diffbind
normalization
chipseq
updated 2.3 years ago by
Rory Stark
★ 4.6k • written 5.0 years ago by
ajeet
• 0
2
votes
4
replies
1.2k
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind
Chipseq
spike-ins
updated 2.3 years ago by
Rory Stark
★ 4.6k • written 3.2 years ago by
Konstantin Okonechnikov
▴ 40
4
votes
3
replies
561
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind
block
regression
deseq2
chipseq
updated 2.3 years ago by
Rory Stark
★ 4.6k • written 3.3 years ago by
melnuesch
▴ 10
1
vote
3
replies
1.9k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind
chipseq
chipqc
updated 2.3 years ago by
Rory Stark
★ 4.6k • written 4.9 years ago by
bioinfouser2
▴ 10
1
vote
9
replies
1.5k
views
Spike-in normalization in EdgeR
CUTandRUN
edgeR
Normalization
SpikeIn
ChIPSeq
updated 10 weeks ago by
Bogdan
▴ 660 • written 2.3 years ago by
Hesh
▴ 10
1
vote
1
reply
1.0k
views
News:
Extensive updates in DiffBind 3.0
Normalization
ATACSeq
ChIPSeq
DiffBind
chipseq
written 2.3 years ago by
Rory Stark
★ 4.6k
0
votes
1
reply
781
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR
ChIPs
ChIPseeker
ChIPSeq
chipseq
updated 2.3 years ago by
James W. MacDonald
62k • written 2.3 years ago by
ret28
• 0
1
vote
7
replies
1.1k
views
DiffBind: dealing with replicates
diffbind
chipseq
updated 2.9 years ago by
Rory Stark
★ 4.6k • written 2.9 years ago by
hkitano
• 0
0
votes
1
reply
482
views
Retrieving ChIP-seq data from Geo database
ChIPseq
GEO data base
updated 3.0 years ago by
James W. MacDonald
62k • written 3.0 years ago by
poodap127
• 0
0
votes
1
reply
409
views
DiffBind MA plot annotate promoter regions with different colour
diffbind
chipseq
rorystark
updated 3.0 years ago by
Rory Stark
★ 4.6k • written 3.0 years ago by
bioinfouser2
▴ 10
0
votes
0
replies
345
views
How to change the text size for the names of ColAttributes
diffbind
colattributes
chipseq
cex
3.2 years ago
researcher
• 0
0
votes
0
replies
390
views
ChIPQC makes a neverending loop while using all chromosomes
chipqc
chipseq
ChIPQC
3.4 years ago
laura.mannarino
▴ 20
0
votes
1
reply
547
views
diffBind analysis: only one replicate
diffbind
chipseq
updated 3.5 years ago by
Rory Stark
★ 4.6k • written 3.5 years ago by
danielaperry2015
• 0
1
vote
3
replies
662
views
Error: package or namespace load failed for 'ChIPseeker': 'TxDb.Hsapiens.UCSC.hg19.knownGene' is not exported from 'namespace: TxDb.Hsapiens.UCSC.hg1…
chipseq
chipseeker
R
Bioconductor
updated 3.6 years ago by
Martin Morgan
25k • written 3.6 years ago by
charlesgwellem
▴ 10
0
votes
5
replies
687
views
process bed/bedGraph files with the same coordinates for all the samples
ChIPSeq
3.6 years ago
Kath
• 0
2
votes
2
replies
1.6k
views
DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind
R
MAplot
Chipseq
updated 3.7 years ago by
Rory Stark
★ 4.6k • written 3.7 years ago by
melnuesch
▴ 10
0
votes
3
replies
574
views
Diffbind affinity based analysis
Diffbind
ChIPseq
Affinity analysis
Differentially bound sites
occupancy analysis
updated 3.7 years ago by
Rory Stark
★ 4.6k • written 3.7 years ago by
rapmic
• 0
0
votes
0
replies
847
views
Error while annotating with Chipseeker
annotation
chipseq
4.0 years ago
hamaor
• 0
0
votes
0
replies
769
views
How to use ChIPseeker for getting genebody annotations.
chipseeker
chipseq
4.1 years ago
bioinfouser2
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 and heatmap for multiple comparisons
by
artem.vorobyev
• 0
this I already did. My question is how to visualize differentially expressed genes on the heatmap for all 3 groups (healty->lesion->treat…
Comment: athPkgBuilder data source :missing probesets
by
nicklesteele532
• 0
> >>> > >>> How to handle the one probeset to multiple locus mappings? I can > >think 3 > >>> possible solutions: > >>> 1. pick the "best" …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
> sum(width(gr_toexclude)) [1] 2713499861 I excluded everything which was not locus. If small rna locus is from 2000 to 4000 and next locu…
Comment: Why in Bioconductor community people rarely upvote questions?
by
Hervé Pagès
16k
BTW I fail to see how the lack of upvotes to a question would be discouraging as long as you get a good answer. OTOH I can see how failing …
Answer: DESeq2 and heatmap for multiple comparisons
by
swbarnes2
★ 1.2k
If you want to know what genes are different between lesion and treated, compare them to each other.
Votes
Comment: recount 3 protect read length metadata
Answer: Doubts about manipulation and annotation of microarray files deposited at GEO
C: Batch correction in DESeq2
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
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