Showing : ChIPseq • reset
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105
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
23 days ago jared.andrews07 ▴ 30
1
vote
1
reply
251
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 10 weeks ago by 64k • written 10 weeks ago by • 0
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0
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139
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
10 weeks ago franciscrick41 • 0
2
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14
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771
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 3 months ago by 64k • written 3 months ago by ▴ 10
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5
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1.3k
views
diffbind
DiffBind chipseq
updated 4 months ago by ★ 5.1k • written 4 months ago by • 0
1
vote
4
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658
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 6 months ago by ★ 5.1k • written 6 months ago by • 0
0
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2
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429
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 7 months ago by ▴ 70 • written 7 months ago by ▴ 140
5
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8
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742
views
Help with error install csaw
ChIPSeq ATACSeq
updated 8 months ago by • 0 • written 8 months ago by • 0
0
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2
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740
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
8 months ago Giulia • 0
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0
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302
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
8 months ago Giulia • 0
1
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2
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700
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how i can get the name of genes in pathway?
chipseq ChIPseeker
9 months ago chavaleab • 0
1
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3
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484
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
9 months ago stacy.genovese • 0
1
vote
4
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842
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
11 months ago • updated 10 months ago stacy.genovese • 0
0
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2
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578
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
12 months ago stacy.genovese • 0
0
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1
reply
705
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 14 months ago by ★ 5.1k • written 14 months ago by • 0
6
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3
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1.1k
views
MEDIPS for chIP-Seq
ChIPSeq
written 16 months ago by ▴ 30
0
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7
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1.5k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 16 months ago by ▴ 40 • written 3.6 years ago by ▴ 10
0
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1
reply
726
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
16 months ago Jenny Drnevich ★ 2.0k
0
votes
0
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546
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intron coordination and annotation
ChIPSeq
updated 16 months ago by ★ 3.6k • written 17 months ago by • 0
0
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0
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641
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Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
18 months ago xubeisi • 0
0
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1
reply
584
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 19 months ago by ★ 1.3k • written 19 months ago by • 0
0
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3
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825
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DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 19 months ago by ★ 5.1k • written 19 months ago by • 0
0
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0
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560
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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
19 months ago Swadha • 0
0
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1
reply
697
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 20 months ago by ★ 5.1k • written 21 months ago by • 0
1
vote
2
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1.0k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 21 months ago by ★ 5.1k • written 21 months ago by • 0
1
vote
1
reply
837
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 23 months ago by ★ 5.1k • written 24 months ago by • 0
0
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0
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632
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.0 years ago Nadav • 0
0
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0
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795
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
2.2 years ago Drew • 0
0
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6
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1.4k
views
cel files with affy library
ChIPSeq
updated 2.3 years ago by • 0 • written 2.3 years ago by • 0
3
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12
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2.8k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 2.3 years ago by ★ 5.1k • written 4.2 years ago by ▴ 20
0
votes
2
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961
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
2.4 years ago • updated 2.3 years ago maria.soler • 0
2
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3
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1.1k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 2.3 years ago by ▴ 20 • written 2.4 years ago by • 0
5
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8
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1.9k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 18 months ago by ▴ 20 • written 2.4 years ago by ▴ 30
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1
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1.6k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 2.5 years ago by 64k • written 2.5 years ago by ▴ 270
2
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5
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2.7k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 12 months ago by • 0 • written 2.5 years ago by ★ 5.1k
2
votes
4
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1.1k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
2.6 years ago • updated 2.5 years ago richardallenfriedmanbrooklyn • 0
0
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0
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1.5k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
2.7 years ago Goku • 0
2
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6
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1.2k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
2.7 years ago Goku • 0
0
votes
3
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890
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 2.7 years ago by ▴ 740 • written 2.8 years ago by • 0
1
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4
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1.1k
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DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
2.8 years ago SFn • 0
0
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11
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1.7k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 2.8 years ago by • 0 • written 2.9 years ago by • 0
0
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2
replies
928
views
DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
3.0 years ago indi97 • 0
2
votes
2
replies
2.2k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
3.1 years ago • updated 2.8 years ago Mar Mar ▴ 20
1
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4
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1.8k
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 3.1 years ago by ★ 5.1k • written 5.9 years ago by • 0
2
votes
4
replies
1.6k
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind Chipseq spike-ins
updated 3.1 years ago by ★ 5.1k • written 4.1 years ago by ▴ 40
4
votes
3
replies
846
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 3.1 years ago by ★ 5.1k • written 4.1 years ago by ▴ 10
1
vote
3
replies
2.5k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind chipseq chipqc
updated 3.1 years ago by ★ 5.1k • written 5.8 years ago by ▴ 10
1
vote
9
replies
2.5k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 12 months ago by ▴ 670 • written 3.1 years ago by ▴ 10
1
vote
1
reply
1.4k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 3.1 years ago by ★ 5.1k
0
votes
1
reply
1.2k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 3.1 years ago by 64k • written 3.1 years ago by • 0
50 results • Page 1 of 1
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Comment: Correct the batch effect in methylation analysis in R by kyj2226 • 0
Thank you for your response Gordon :) I've already run the code below, just add batch to the limma linear model design <- model.matri…
Answer: Correct the batch effect in methylation analysis in R by Gordon Smyth 49k
You should not apply batch correction functions like harman before a limma analysis. Instead, just add `batch` to the limma linear model. …
Answer: Agilent Microarray Gene Oncology analysis gone wrong by Gordon Smyth 49k
Your use of `coef=1` is incorrect, for reasons explained in the limma User's Guide. If you had simply left `coef` at the default, then thin…
Comment: Normalised counts from RUVg in RUVSeq by Shaimaa Gamal • 0
Hello I was wondering if I should use ruv-corrected counts and ruv lib sizes to create a DGE object that can be used later for DE analysis …
Comment: enrichGOgradient color change by James W. MacDonald 64k
You could look at my answer and extrapolate from there.
Votes
Answer: Correct the batch effect in methylation analysis in R
Answer: enrichGOgradient color change
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
Answer: Filter genes by expression for voomLmFit
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