Showing : ChIpseq • reset
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74
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what is the sampleFiles
chipseq
updated 3 days ago by 65k • written 3 days ago by • 0
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140
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
10 weeks ago nilanjanamani88 • 0
1
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3
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365
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 11 weeks ago by 41k • written 12 weeks ago by • 0
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0
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161
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
1
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3
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1.8k
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DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 4 months ago by ★ 5.1k • written 6.5 years ago by • 0
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0
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315
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
5 months ago jared.andrews07 ▴ 30
1
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1
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425
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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 6 months ago by 65k • written 6 months ago by • 0
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270
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
6 months ago franciscrick41 • 0
2
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14
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1.1k
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 7 months ago by 65k • written 8 months ago by ▴ 10
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5
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2.9k
views
diffbind
DiffBind chipseq
updated 8 months ago by ★ 5.1k • written 8 months ago by • 0
1
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4
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987
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 10 months ago by ★ 5.1k • written 11 months ago by • 0
0
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1
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1.1k
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diffBind analysis: only one replicate
diffbind chipseq
updated 11 months ago by • 0 • written 4.6 years ago by • 0
0
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2
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588
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 11 months ago by ▴ 70 • written 12 months ago by ▴ 140
5
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8
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994
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Help with error install csaw
ChIPSeq ATACSeq
written 12 months ago by • 0
0
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2
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1.1k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
13 months ago Giulia • 0
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0
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438
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
13 months ago Giulia • 0
1
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2
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1.0k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
13 months ago chavaleab • 0
2
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4
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3.4k
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Error in DESeqDataSetFromHTSeqCount: Gene IDs (first column) differ between files.
chipseq deseq2 htseqcounts
updated 13 months ago by ▴ 10 • written 7.2 years ago by ▴ 40
1
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3
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671
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Only getting 10 peaks from mac2 callpeak
ChIPSeq
14 months ago stacy.genovese • 0
1
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4
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1.1k
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
15 months ago stacy.genovese • 0
2
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5
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3.3k
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 16 months ago by • 0 • written 2.9 years ago by ★ 5.1k
1
vote
9
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2.9k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 16 months ago by ▴ 670 • written 3.5 years ago by ▴ 10
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2
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750
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
17 months ago stacy.genovese • 0
6
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3
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1.3k
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MEDIPS for chIP-Seq
ChIPSeq
written 20 months ago by ▴ 30
0
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1
reply
854
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DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 18 months ago by ★ 5.1k • written 18 months ago by • 0
0
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7
replies
1.8k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 20 months ago by ▴ 40 • written 4.0 years ago by ▴ 10
0
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1
reply
891
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
21 months ago • updated 20 months ago Jenny Drnevich ★ 2.0k
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680
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intron coordination and annotation
ChIPSeq
updated 21 months ago by ★ 4.0k • written 21 months ago by • 0
0
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0
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773
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Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
22 months ago xubeisi • 0
5
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8
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2.1k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 22 months ago by ▴ 20 • written 2.8 years ago by ▴ 30
0
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1
reply
693
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 23 months ago by ★ 1.3k • written 23 months ago by • 0
0
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3
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994
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DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 23 months ago by ★ 5.1k • written 23 months ago by • 0
0
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0
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677
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
24 months ago Swadha • 0
0
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1
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843
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 2.0 years ago by ★ 5.1k • written 2.1 years ago by • 0
1
vote
2
replies
1.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.1 years ago by ★ 5.1k • written 2.1 years ago by • 0
1
vote
1
reply
998
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 2.3 years ago by ★ 5.1k • written 2.3 years ago by • 0
0
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0
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725
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.4 years ago Nadav • 0
0
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0
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890
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
2.5 years ago Drew • 0
2
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3
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1.4k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 2.6 years ago by ▴ 20 • written 2.7 years ago by • 0
0
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6
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1.6k
views
cel files with affy library
ChIPSeq
updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
3
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12
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3.3k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 2.7 years ago by ★ 5.1k • written 4.6 years ago by ▴ 20
0
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2
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1.1k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
2.7 years ago maria.soler • 0
2
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4
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1.2k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
2.9 years ago richardallenfriedmanbrooklyn ▴ 20
0
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1
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1.8k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 2.9 years ago by 65k • written 2.9 years ago by ▴ 270
2
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3
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2.3k
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Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind chipseq counts peaks bedtools
updated 3.0 years ago by ★ 5.1k • written 6.0 years ago by ▴ 10
2
votes
6
replies
1.4k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
3.1 years ago Goku • 0
0
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0
replies
1.7k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
3.1 years ago Goku • 0
0
votes
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 3.1 years ago by ▴ 770 • written 3.1 years ago by • 0
1
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4
replies
1.3k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
3.2 years ago • updated 3.1 years ago SFn • 0
0
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11
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2.0k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 3.2 years ago by • 0 • written 3.3 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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