Showing : ChIpseq • reset
6
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5
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1.8k
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MEDIPS for chIP-Seq
ChIPSeq
written 2.4 years ago by ▴ 30
0
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0
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136
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ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
6 weeks ago user_bioinfo • 0
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0
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220
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
3 months ago Alejandro • 0
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0
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377
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
5 months ago gamma.jian ▴ 10
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0
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370
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
7 months ago yvonneh • 0
0
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1
reply
312
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what is the sampleFiles
chipseq
updated 8 months ago by 67k • written 8 months ago by • 0
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0
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489
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
10 months ago nilanjanamani88 • 0
1
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3
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693
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 10 months ago by 43k • written 10 months ago by • 0
0
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0
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370
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
11 months ago frueher • 0
0
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0
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640
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
13 months ago jared.andrews07 ▴ 30
1
vote
1
reply
781
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 14 months ago by 67k • written 14 months ago by • 0
0
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0
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485
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
14 months ago franciscrick41 • 0
2
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14
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1.7k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 16 months ago by 67k • written 16 months ago by ▴ 10
0
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5
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6.5k
views
diffbind
DiffBind chipseq
updated 17 months ago by ★ 5.2k • written 17 months ago by • 0
1
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4
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1.7k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 18 months ago by ★ 5.2k • written 19 months ago by • 0
0
votes
2
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904
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 20 months ago by ▴ 70 • written 20 months ago by ▴ 140
5
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8
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1.4k
views
Help with error install csaw
ChIPSeq ATACSeq
written 21 months ago by ▴ 20
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2
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1.6k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
21 months ago Giulia • 0
0
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0
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613
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
21 months ago Giulia • 0
1
vote
2
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1.4k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
21 months ago chavaleab • 0
1
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3
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969
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Only getting 10 peaks from mac2 callpeak
ChIPSeq
22 months ago stacy.genovese • 0
1
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4
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1.6k
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
23 months ago stacy.genovese • 0
0
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2
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1.0k
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
2.1 years ago stacy.genovese • 0
0
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1
reply
1.1k
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DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 2.2 years ago by ★ 5.2k • written 2.2 years ago by • 0
0
votes
7
replies
2.3k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 2.4 years ago by ▴ 40 • written 4.7 years ago by ▴ 10
0
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1
reply
1.2k
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
2.4 years ago Jenny Drnevich ★ 2.0k
0
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0
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946
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intron coordination and annotation
ChIPSeq
updated 2.4 years ago by ★ 4.6k • written 2.4 years ago by • 0
0
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0
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1.0k
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
2.5 years ago xubeisi • 0
0
votes
1
reply
878
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.6 years ago by ★ 1.3k • written 2.6 years ago by • 0
0
votes
3
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1.3k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 2.6 years ago by ★ 5.2k • written 2.6 years ago by • 0
0
votes
0
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873
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
2.6 years ago Swadha • 0
0
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1
reply
1.1k
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 2.7 years ago by ★ 5.2k • written 2.8 years ago by • 0
1
vote
2
replies
1.6k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.8 years ago by ★ 5.2k • written 2.8 years ago by • 0
1
vote
1
reply
1.3k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 3.0 years ago by ★ 5.2k • written 3.0 years ago by • 0
0
votes
0
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951
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.0 years ago Nadav • 0
0
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0
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1.1k
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
3.2 years ago Drew • 0
0
votes
6
replies
2.3k
views
cel files with affy library
ChIPSeq
updated 3.4 years ago by • 0 • written 3.4 years ago by • 0
3
votes
12
replies
4.2k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 3.4 years ago by ★ 5.2k • written 5.3 years ago by ▴ 20
0
votes
2
replies
1.4k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
3.4 years ago maria.soler • 0
2
votes
3
replies
1.9k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 3.3 years ago by ▴ 20 • written 3.4 years ago by • 0
5
votes
8
replies
2.7k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.5 years ago by ▴ 20 • written 3.4 years ago by ▴ 30
0
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1
reply
2.2k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 3.6 years ago by 67k • written 3.6 years ago by ▴ 290
2
votes
5
replies
4.5k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.0 years ago by • 0 • written 3.6 years ago by ★ 5.2k
2
votes
4
replies
1.6k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.6 years ago richardallenfriedmanbrooklyn ▴ 30
0
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0
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2.0k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
3.7 years ago Goku • 0
2
votes
6
replies
1.8k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
3.7 years ago Goku • 0
0
votes
3
replies
1.2k
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 3.8 years ago by ▴ 780 • written 3.8 years ago by • 0
1
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4
replies
1.7k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
3.9 years ago • updated 3.8 years ago SFn • 0
0
votes
11
replies
2.4k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 3.9 years ago by • 0 • written 3.9 years ago by • 0
0
votes
2
replies
1.4k
views
DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
4.1 years ago • updated 4.0 years ago indi97 • 0
50 results • Page 1 of 1
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Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200
Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k
Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…
Votes
Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
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