Showing : ChipSeq • reset
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100
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what is the sampleFiles
chipseq
updated 9 days ago by 65k • written 9 days ago by • 0
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0
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152
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
11 weeks ago nilanjanamani88 • 0
1
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3
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375
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 12 weeks ago by 41k • written 3 months ago by • 0
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0
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168
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
0
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0
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321
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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
vote
1
reply
439
views
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
0
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0
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274
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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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1.1k
views
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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2.9k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
1
vote
4
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997
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 10 months ago by ★ 5.2k • written 11 months ago by • 0
0
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2
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593
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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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1.0k
views
Help with error install csaw
ChIPSeq ATACSeq
written 13 months ago by • 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
13 months ago Giulia • 0
0
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0
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443
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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
1
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3
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678
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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
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
15 months ago stacy.genovese • 0
0
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2
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763
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
17 months ago stacy.genovese • 0
0
votes
1
reply
863
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 18 months ago by ★ 5.2k • written 18 months ago by • 0
6
votes
3
replies
1.3k
views
MEDIPS for chIP-Seq
ChIPSeq
written 20 months ago by ▴ 30
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
votes
1
reply
898
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
21 months ago Jenny Drnevich ★ 2.0k
0
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0
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688
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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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786
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
22 months ago xubeisi • 0
0
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1
reply
700
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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1.0k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 23 months ago by ★ 5.2k • written 23 months ago by • 0
0
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0
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684
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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
24 months ago Swadha • 0
0
votes
1
reply
853
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 2.1 years ago by ★ 5.2k • written 2.1 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 ★ 5.2k • written 2.1 years ago by • 0
1
vote
1
reply
1.0k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 2.3 years ago by ★ 5.2k • written 2.4 years ago by • 0
0
votes
0
replies
734
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.4 years ago Nadav • 0
0
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0
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899
views
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
replies
1.7k
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 ★ 5.2k • written 4.6 years ago by ▴ 20
0
votes
2
replies
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
votes
3
replies
1.4k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 2.6 years ago by ▴ 20 • written 2.8 years ago by • 0
5
votes
8
replies
2.2k
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
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 ▴ 280
2
votes
5
replies
3.3k
views
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 ★ 5.2k
2
votes
4
replies
1.2k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.0 years ago • updated 2.9 years ago richardallenfriedmanbrooklyn ▴ 20
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
2
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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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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 3.1 years ago by ▴ 780 • 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
replies
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
0
votes
2
replies
1.1k
views
DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
3.4 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 3.2 years ago Mar Mar ▴ 20
1
vote
4
replies
2.0k
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 3.5 years ago by ★ 5.2k • written 6.3 years ago by • 0
2
votes
4
replies
1.7k
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind Chipseq spike-ins
updated 3.5 years ago by ★ 5.2k • written 4.5 years ago by ▴ 40
4
votes
3
replies
990
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 3.5 years ago by ★ 5.2k • written 4.5 years ago by ▴ 10
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Hi, Yes, I've tried this, but I am not sure if it is possible to assign `bquote` values to the names of a vector. In particular, if I use…
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