Showing : ChIPSeq • reset
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103
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
24 days ago yvonneh • 0
0
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1
reply
140
views
what is the sampleFiles
chipseq
updated 5 weeks ago by 66k • written 5 weeks ago by • 0
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0
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210
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
3 months ago nilanjanamani88 • 0
1
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3
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439
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 3 months ago by 42k • written 4 months ago by • 0
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0
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195
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
4 months ago frueher • 0
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0
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355
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
480
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 8 months ago by 66k • written 8 months ago by • 0
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0
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301
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
8 months ago franciscrick41 • 0
2
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14
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1.2k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 9 months ago by 66k • written 9 months ago by ▴ 10
0
votes
5
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3.3k
views
diffbind
DiffBind chipseq
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
1
vote
4
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1.1k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 11 months ago by ★ 5.2k • written 12 months ago by • 0
0
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2
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634
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 13 months ago by ▴ 70 • written 13 months ago by ▴ 140
5
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8
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1.1k
views
Help with error install csaw
ChIPSeq ATACSeq
written 14 months ago by ▴ 10
0
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0
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462
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
14 months ago Giulia • 0
0
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2
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1.1k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
14 months ago Giulia • 0
1
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2
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1.1k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
14 months ago chavaleab • 0
1
vote
3
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717
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Only getting 10 peaks from mac2 callpeak
ChIPSeq
15 months ago stacy.genovese • 0
1
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4
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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
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2
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796
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
18 months ago stacy.genovese • 0
0
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1
reply
897
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DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 19 months ago by ★ 5.2k • written 19 months ago by • 0
6
votes
3
replies
1.4k
views
MEDIPS for chIP-Seq
ChIPSeq
written 22 months ago by ▴ 30
0
votes
1
reply
918
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
22 months ago Jenny Drnevich ★ 2.0k
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0
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714
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intron coordination and annotation
ChIPSeq
updated 22 months ago by ★ 4.2k • written 22 months ago by • 0
0
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0
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837
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Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
23 months ago xubeisi • 0
0
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1
reply
725
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.0 years ago by ★ 1.3k • written 2.0 years ago by • 0
0
votes
3
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1.0k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 2.0 years ago by ★ 5.2k • written 2.0 years ago by • 0
0
votes
0
replies
709
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
1
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2
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1.3k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.2 years ago by ★ 5.2k • written 2.2 years ago by • 0
0
votes
1
reply
886
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 2.1 years ago by ★ 5.2k • written 2.2 years ago by • 0
1
vote
1
reply
1.1k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by • 0
0
votes
0
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758
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.5 years ago Nadav • 0
0
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0
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919
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
2.6 years ago Drew • 0
0
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6
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1.8k
views
cel files with affy library
ChIPSeq
updated 2.8 years ago by • 0 • written 2.8 years ago by • 0
0
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2
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1.2k
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Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
2.8 years ago maria.soler • 0
2
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3
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1.4k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 2.7 years ago by ▴ 20 • written 2.8 years ago by • 0
5
votes
8
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2.2k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 23 months ago by ▴ 20 • written 2.9 years ago by ▴ 30
0
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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 66k • written 3.0 years ago by ▴ 290
2
votes
5
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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 • 0 • written 3.0 years ago by ★ 5.2k
2
votes
4
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1.3k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.0 years ago richardallenfriedmanbrooklyn ▴ 20
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0
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1.7k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
3.2 years ago Goku • 0
2
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6
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1.5k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
3.2 years ago Goku • 0
0
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3
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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 ▴ 780 • written 3.2 years ago by • 0
1
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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
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11
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2.1k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 3.3 years ago by • 0 • written 3.4 years ago by • 0
0
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2
replies
1.1k
views
DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
3.5 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
1
reply
1.6k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 3.6 years ago by ★ 5.2k
1
vote
9
replies
3.1k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 18 months ago by ▴ 670 • written 3.6 years ago by ▴ 10
0
votes
1
reply
1.5k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 3.6 years ago by 66k • written 3.6 years ago by • 0
0
votes
7
replies
1.9k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 21 months ago by ▴ 40 • written 4.1 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by BioinfGuru ▴ 30
I would use biomaRt. This is what happens when annotation occurs to early. If possible I would run the DEG analysis on the original output…
Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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