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ChIPseq
•
reset
0
votes
0
replies
14
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno
ChIPSeq
17 hours ago
Abhilansh
• 0
0
votes
3
replies
79
views
DiffBind on static peak set for all samples
ChIPSeq
DiffBind
updated 2 days ago by
Rory Stark
★ 4.4k • written 3 days ago by
Drew
• 0
0
votes
0
replies
59
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq
ChIPseeker
18 days ago
Swadha
• 0
0
votes
1
reply
142
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq
DiffBind
updated 5 weeks ago by
Rory Stark
★ 4.4k • written 9 weeks ago by
rita.rebollo
• 0
1
vote
2
replies
183
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw
edger
tmm
chipseq
updated 8 weeks ago by
Rory Stark
★ 4.4k • written 8 weeks ago by
maria.soler
• 0
1
vote
1
reply
236
views
DiffBind scoreCol value question
DiffBind
ChIPSeq
chipseq
updated 4 months ago by
Rory Stark
★ 4.4k • written 5 months ago by
erbrocato
• 0
0
votes
0
replies
140
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks
ChIPpeakAnno
chipseq
5 months ago
Nadav
• 0
0
votes
0
replies
179
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind
ChIPSeq
Normalization
SpikeIn
7 months ago
Drew
• 0
0
votes
6
replies
452
views
cel files with affy library
ChIPSeq
updated 9 months ago by
almaza24map
• 0 • written 9 months ago by
scipio04
• 0
3
votes
12
replies
1.0k
views
Is it possible to change how DiffBind merge peaks?
DiffBind
ChIPseq
updated 9 months ago by
Rory Stark
★ 4.4k • written 2.7 years ago by
zhenfeng.liu1
▴ 20
0
votes
2
replies
330
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq
SpikeIn
edgeR
Normalization
9 months ago
maria.soler
• 0
2
votes
3
replies
414
views
An error using Diffbind plotprofile
ChIPSeq
profileplyr
DiffBind
updated 8 months ago by
doug.barrows
▴ 20 • written 9 months ago by
zhuyi05
• 0
5
votes
7
replies
647
views
how to construct a DBA object from count matrix
ChIPSeq
ATACSeq
differentially_occupied
DiffBind
updated 6 weeks ago by
xlu.cpu
• 0 • written 10 months ago by
pegah.taklifi
▴ 30
0
votes
1
reply
569
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq
SICER2
DiffBind
MACS2
offtopic
updated 11 months ago by
James W. MacDonald
59k • written 11 months ago by
Yuan Tian
▴ 250
1
vote
2
replies
733
views
News:
New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr
ATACSeq
DiffBind
ComplexHeatmap
ChIPSeq
11 months ago • updated 8 months ago
Rory Stark
★ 4.4k
2
votes
4
replies
434
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq
csaw;
crosscorrelation
12 months ago • updated 11 months ago
richardallenfriedmanbrooklyn
• 0
0
votes
0
replies
499
views
Blacklist error at dba.analyze(dbObj)
DiffBind
ChIPSeq
13 months ago
Goku
• 0
2
votes
6
replies
479
views
Error with dba.count(dbObj) in DiffBind
DiffBind
ChIPSeq
13 months ago
Goku
• 0
0
votes
3
replies
395
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 14 months ago by
Basti
▴ 280 • written 14 months ago by
Mick
• 0
1
vote
4
replies
466
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq
DiffBind
ExperimentalDesign
15 months ago • updated 14 months ago
SFn
• 0
0
votes
11
replies
802
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq
ChIPSeqSpike
updated 15 months ago by
nicolas.descostes
• 0 • written 16 months ago by
Ainul
• 0
0
votes
2
replies
383
views
DiffBind Error When using dba.count()
ChIP-Rx
DiffBind
chipseq
17 months ago
indi97
• 0
2
votes
2
replies
1.2k
views
ChIP seeker annotation error
DiffBind
chipseq
ChIPseeker
ChipDb
annotation
18 months ago • updated 15 months ago
Mar Mar
▴ 20
1
vote
4
replies
1.1k
views
MAnorm output as DiffBind input.
MAnorm
diffbind
normalization
chipseq
updated 18 months ago by
Rory Stark
★ 4.4k • written 4.3 years ago by
ajeet
• 0
2
votes
4
replies
907
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind
Chipseq
spike-ins
updated 18 months ago by
Rory Stark
★ 4.4k • written 2.5 years ago by
Konstantin Okonechnikov
▴ 30
4
votes
3
replies
388
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind
block
regression
deseq2
chipseq
updated 18 months ago by
Rory Stark
★ 4.4k • written 2.5 years ago by
melnuesch
▴ 10
1
vote
3
replies
1.6k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind
chipseq
chipqc
updated 18 months ago by
Rory Stark
★ 4.4k • written 4.2 years ago by
bioinfouser2
▴ 10
1
vote
8
replies
939
views
Spike-in normalization in EdgeR
CUTandRUN
edgeR
Normalization
SpikeIn
ChIPSeq
18 months ago
Hesh
• 0
1
vote
1
reply
817
views
News:
Extensive updates in DiffBind 3.0
Normalization
ATACSeq
ChIPSeq
DiffBind
chipseq
written 18 months ago by
Rory Stark
★ 4.4k
0
votes
1
reply
429
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR
ChIPs
ChIPseeker
ChIPSeq
chipseq
updated 18 months ago by
James W. MacDonald
59k • written 18 months ago by
ret28
• 0
0
votes
1
reply
403
views
CHIPQC error regarding BiocParallel
CHIPQC
Diffbind
chipseq
rory stark
Thomas Carroll
updated 2.1 years ago by
Martin Morgan
25k • written 2.1 years ago by
bioinfouser2
▴ 10
1
vote
7
replies
653
views
DiffBind: dealing with replicates
diffbind
chipseq
updated 2.2 years ago by
Rory Stark
★ 4.4k • written 2.2 years ago by
hkitano
• 0
0
votes
1
reply
298
views
Retrieving ChIP-seq data from Geo database
ChIPseq
GEO data base
updated 2.2 years ago by
James W. MacDonald
59k • written 2.2 years ago by
poodap127
• 0
0
votes
1
reply
271
views
DiffBind MA plot annotate promoter regions with different colour
diffbind
chipseq
rorystark
updated 2.2 years ago by
Rory Stark
★ 4.4k • written 2.3 years ago by
bioinfouser2
▴ 10
0
votes
0
replies
233
views
How to change the text size for the names of ColAttributes
diffbind
colattributes
chipseq
cex
2.5 years ago • updated 2.4 years ago
researcher
• 0
0
votes
0
replies
276
views
ChIPQC makes a neverending loop while using all chromosomes
chipqc
chipseq
ChIPQC
2.7 years ago
laura.mannarino
▴ 20
0
votes
1
reply
326
views
diffBind analysis: only one replicate
diffbind
chipseq
updated 2.7 years ago by
Rory Stark
★ 4.4k • written 2.7 years ago by
danielaperry2015
• 0
1
vote
3
replies
494
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 2.9 years ago by
Martin Morgan
25k • written 2.9 years ago by
charlesgwellem
▴ 10
0
votes
5
replies
490
views
process bed/bedGraph files with the same coordinates for all the samples
ChIPSeq
2.9 years ago
Kath
• 0
2
votes
2
replies
1.2k
views
DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind
R
MAplot
Chipseq
updated 3.0 years ago by
Rory Stark
★ 4.4k • written 3.0 years ago by
melnuesch
▴ 10
0
votes
3
replies
436
views
Diffbind affinity based analysis
Diffbind
ChIPseq
Affinity analysis
Differentially bound sites
occupancy analysis
updated 3.0 years ago by
Rory Stark
★ 4.4k • written 3.0 years ago by
rapmic
• 0
0
votes
0
replies
719
views
Error while annotating with Chipseeker
annotation
chipseq
3.2 years ago
hamaor
• 0
0
votes
0
replies
633
views
How to use ChIPseeker for getting genebody annotations.
chipseeker
chipseq
3.4 years ago
bioinfouser2
▴ 10
3
votes
7
replies
1.8k
views
DEseq2 for differential binding analysis ChIP seq
deseq2
diffbind
csaw
greylistchip
chipseq
updated 3.4 years ago by
Michael Love
36k • written 3.4 years ago by
Yonatan Amzaleg
• 0
3
votes
2
replies
663
views
diffbind finding not differential site
diffbind
chipseq
histone chip-seq
differential binding analysis
updated 3.5 years ago by
Rory Stark
★ 4.4k • written 3.6 years ago by
woongjaej
• 0
3
votes
4
replies
1.1k
views
ChIPseeker/Question about ''annoatePeak' function and for Bioconductor AnnotationData Packages for L.japonicus
chipseeker
Bioconductor AnnotationData Packages
Lotus japonicus
ChIPseq
updated 3.6 years ago by
James W. MacDonald
59k • written 3.6 years ago by
egbastakis
• 0
0
votes
7
replies
689
views
ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno
chipseq
R
updated 3.7 years ago by
Ou, Jianhong
★ 1.3k • written 3.7 years ago by
94133
• 0
1
vote
3
replies
880
views
How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker
chipseq
updated 3.7 years ago by
Guangchuang Yu
★ 1.2k • written 3.8 years ago by
bioinfouser2
▴ 10
0
votes
0
replies
462
views
Cannot open file because of connection error
systemArgs
chipseq
working directory
3.8 years ago
hallie.s
• 0
0
votes
0
replies
549
views
Job:
2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job
rna-seq
chipseq
gsea
python
Job
3.8 years ago
l.brown
▴ 10
50 results • Page
1 of 1
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Replies
Comment: Ensembl plants at annotationHub?
by
karenserrano
• 0
Hi Johannes, Could I request the same EnsDb creation for Medicago truncatula? Thank you very much, Karen
Answer: EnrichGO not working with db created from annotationhub
by
Guido Hooiveld
★ 3.2k
Did you notice the first message that was returned after you ran `enrichGO()`? Thus: `--> No gene can be mapped....` This basically means…
Comment: DiffBind GreyListChIP error: Error: BiocParallel errors
by
ksong
• 0
Hello my friends, I have exactly the same issue. May I ask if you have already solve this problem? I have tried `library(BiocParallel) regi…
Comment: cellCounts() function floating point error
by
Wei Shi
★ 3.3k
Yes we are currently working on generating a small example for cellCounts.
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
by
ksong
• 0
Hi Dr Sudbery, yes I found looking at the coverage in IGV helps a lot. I did find some differences between CDS and UTR and between samples.…
Votes
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
C: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o
Comment: Diffbind dba$binding slot finding Chr21 for an MM10 dataset
Answer: Handling NA values in limma's voom design matrix
Answer: Handling NA values in limma's voom design matrix
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