Showing : ChIPseq • reset
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Csaw normalization strategies - general inquiry
ChIPSeq csaw
3 days ago • updated 10 hours ago Luca • 0
6
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5
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1.9k
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MEDIPS for chIP-Seq
ChIPSeq
written 2.5 years ago by ▴ 30
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0
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159
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ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
11 weeks ago user_bioinfo • 0
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250
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
4 months ago Alejandro • 0
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0
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413
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
7 months ago gamma.jian ▴ 10
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0
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410
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
9 months ago yvonneh • 0
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1
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333
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what is the sampleFiles
chipseq
updated 9 months ago by 67k • written 9 months ago by • 0
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0
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526
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
11 months ago nilanjanamani88 • 0
1
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3
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739
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
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0
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400
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
12 months ago frueher • 0
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0
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678
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
14 months ago jared.andrews07 ▴ 30
1
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1
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820
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DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 16 months ago by 67k • written 16 months ago by • 0
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0
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514
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
16 months ago franciscrick41 • 0
2
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14
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1.8k
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 17 months ago by 67k • written 17 months ago by ▴ 10
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5
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6.7k
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diffbind
DiffBind chipseq
updated 18 months ago by ★ 5.2k • written 18 months ago by • 0
1
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4
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1.7k
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 20 months ago by ★ 5.2k • written 20 months ago by • 0
0
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2
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945
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 21 months ago by ▴ 70 • written 21 months ago by ▴ 140
5
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8
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1.5k
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Help with error install csaw
ChIPSeq ATACSeq
written 22 months ago by ▴ 20
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2
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1.7k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
22 months ago Giulia • 0
0
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0
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634
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
22 months ago Giulia • 0
1
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2
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1.5k
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how i can get the name of genes in pathway?
chipseq ChIPseeker
23 months ago chavaleab • 0
1
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3
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1.0k
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Only getting 10 peaks from mac2 callpeak
ChIPSeq
23 months ago stacy.genovese • 0
1
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4
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1.7k
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
2.1 years ago • updated 2.0 years ago stacy.genovese • 0
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2
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1.1k
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
2.2 years ago stacy.genovese • 0
0
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1
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1.1k
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DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 2.3 years ago by ★ 5.2k • written 2.3 years ago by • 0
0
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7
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2.4k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 2.5 years ago by ▴ 40 • written 4.8 years ago by ▴ 10
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1
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1.2k
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
2.5 years ago Jenny Drnevich ★ 2.0k
0
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0
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968
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intron coordination and annotation
ChIPSeq
updated 2.5 years ago by ★ 4.6k • written 2.5 years ago by • 0
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0
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1.0k
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
2.6 years ago xubeisi • 0
0
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1
reply
901
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AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.7 years ago by ★ 1.3k • written 2.7 years ago by • 0
0
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3
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1.4k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by • 0
0
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0
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897
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Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
2.8 years ago Swadha • 0
0
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1
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1.1k
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Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 2.8 years ago by ★ 5.2k • written 2.9 years ago by • 0
1
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2
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1.7k
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Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.9 years ago by ★ 5.2k • written 2.9 years ago by • 0
1
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1
reply
1.3k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 3.1 years ago by ★ 5.2k • written 3.1 years ago by • 0
0
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0
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979
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.1 years ago Nadav • 0
0
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0
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1.1k
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
3.3 years ago Drew • 0
0
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6
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2.4k
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cel files with affy library
ChIPSeq
updated 3.5 years ago by • 0 • written 3.5 years ago by • 0
3
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12
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4.3k
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Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 3.5 years ago by ★ 5.2k • written 5.4 years ago by ▴ 20
0
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2
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1.5k
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Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
3.5 years ago maria.soler • 0
2
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3
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1.9k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 3.4 years ago by ▴ 20 • written 3.5 years ago by • 0
5
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8
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2.8k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.6 years ago by ▴ 20 • written 3.5 years ago by ▴ 30
0
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1
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2.2k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 3.7 years ago by 67k • written 3.7 years ago by ▴ 290
2
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5
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4.6k
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.1 years ago by • 0 • written 3.7 years ago by ★ 5.2k
2
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4
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1.6k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.7 years ago richardallenfriedmanbrooklyn ▴ 30
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0
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2.0k
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Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
3.8 years ago Goku • 0
2
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6
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1.8k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
3.9 years ago • updated 3.8 years ago Goku • 0
0
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3
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1.3k
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 3.9 years ago by ▴ 780 • written 3.9 years ago by • 0
1
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4
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1.7k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
4.0 years ago • updated 3.9 years ago SFn • 0
0
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11
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2.4k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 4.0 years ago by • 0 • written 4.0 years ago by • 0
50 results • Page 1 of 1
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Answer: Selection of correct coefficients or contrasts in DESeq2 by swbarnes2 ★ 1.4k
I think you need to include the design you used, and the command you used to call it. The simplest answer is that your two ways of doing t…
Comment: Csaw normalization strategies - general inquiry by Luca • 0
Hello Aaron, About the IP efficiencies, yes definitely and for us, to complicate this experiment further, these batches were generated by …
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by Quang NN ▴ 10
Thank you ATpoint for your response. In bulkRNAseq, I did have two cell types to compare. But, I want to also see if bulkRNAseq might have …
Answer: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
The choice of variable genes is typically part of a QC process. You select genes that in an unbiased fashion (unbiased because variance cal…
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by ATpoint ★ 4.6k
My take is that RNA-seq (be it bulk or single-cell) is inherently relative. I don't think you can really "compare" the absolute expression …
Votes
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
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