Showing : Chipseq • reset
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79
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
11 days ago yvonneh • 0
0
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1
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127
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what is the sampleFiles
chipseq
updated 27 days ago by 65k • written 27 days ago by • 0
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0
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184
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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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419
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 3 months ago by 42k • written 3 months ago by • 0
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0
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182
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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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1.9k
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DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 5 months ago by ★ 5.2k • written 6.6 years ago by • 0
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0
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340
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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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465
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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 7 months ago by 65k • written 7 months ago by • 0
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0
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292
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
7 months ago franciscrick41 • 0
2
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14
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1.2k
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 8 months ago by 65k • written 8 months ago by ▴ 10
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5
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3.1k
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diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
1
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4
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1.0k
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 11 months ago by ★ 5.2k • written 11 months ago by • 0
0
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1
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1.2k
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diffBind analysis: only one replicate
diffbind chipseq
updated 12 months ago by • 0 • written 4.7 years ago by • 0
0
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2
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619
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 12 months ago by ▴ 70 • written 12 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 13 months ago by ▴ 10
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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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455
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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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1.1k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
14 months ago chavaleab • 0
2
votes
4
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3.4k
views
Error in DESeqDataSetFromHTSeqCount: Gene IDs (first column) differ between files.
chipseq deseq2 htseqcounts
updated 14 months ago by ▴ 10 • written 7.2 years ago by ▴ 40
1
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3
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705
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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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1.2k
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
16 months ago stacy.genovese • 0
2
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5
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3.4k
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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
1
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9
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3.0k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 17 months ago by ▴ 670 • written 3.5 years ago by ▴ 10
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2
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785
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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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1.4k
views
MEDIPS for chIP-Seq
ChIPSeq
written 21 months ago by ▴ 30
0
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1
reply
880
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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
0
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7
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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
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1
reply
909
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
22 months ago • updated 21 months ago Jenny Drnevich ★ 2.0k
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0
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703
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intron coordination and annotation
ChIPSeq
updated 22 months ago by ★ 4.1k • written 22 months ago by • 0
0
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0
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812
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Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
23 months ago xubeisi • 0
5
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8
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2.2k
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how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 23 months ago by ▴ 20 • written 2.8 years ago by ▴ 30
0
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1
reply
718
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 24 months ago by ★ 1.3k • written 24 months ago by • 0
0
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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
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0
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697
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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
2.0 years ago Swadha • 0
0
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1
reply
877
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
2
replies
1.2k
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
1
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1
reply
1.0k
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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747
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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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910
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
2.6 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 2.7 years ago by ▴ 20 • written 2.8 years ago by • 0
0
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6
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1.7k
views
cel files with affy library
ChIPSeq
updated 2.8 years ago by • 0 • written 2.8 years ago by • 0
3
votes
12
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3.4k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 2.8 years ago by ★ 5.2k • written 4.7 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
2.8 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
3.0 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 3.0 years ago by 65k • written 3.0 years ago by ▴ 280
2
votes
3
replies
2.4k
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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 ★ 5.2k • written 6.1 years ago by ▴ 10
2
votes
6
replies
1.5k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
3.1 years ago Goku • 0
0
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0
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1.7k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
3.1 years ago Goku • 0
0
votes
3
replies
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
50 results • Page 1 of 1
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Comment: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by alex.pico ▴ 20
Hi Matthew. Happy to help. The error message you are getting is indeed not very helpful. It's just saying that the CyREST return obj "res" …
Comment: ChipQC 'names' attribute [9] must be the same length as the vector [2]' by bandconductor • 0
thanks! you have saved me so much time
Comment: Problem finding certain variables when importing a public database GSE73103 by Guido Hooiveld ★ 3.9k
FWIW: when I would like to make use of publicly available data, I always use the website to explore which metadata is submitted to GEO (and…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
This is `blockLength=200000`, and providing `seg=seg`? It's alright that it's not identical. In the bootstrapped data, you will now have l…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Thank you, Michael. I used the script shared by you. The genomic distribution of the original and null loci looks like non-stationary. Plea…
Votes
Answer: ChipQC 'names' attribute [9] must be the same length as the vector [2]'
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
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