Showing : ChIPSeq • reset
1
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147
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DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 5 weeks ago by ★ 4.3k • written 6 weeks ago by • 0
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75
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
7 weeks ago Nadav • 0
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0
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115
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
3 months ago Drew • 0
0
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6
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317
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cel files with affy library
ChIPSeq
updated 5 months ago by • 0 • written 5 months ago by • 0
3
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12
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822
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Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 5 months ago by ★ 4.3k • written 2.4 years ago by ▴ 20
0
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2
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262
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Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
6 months ago • updated 5 months ago maria.soler • 0
2
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3
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331
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An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 4 months ago by ▴ 20 • written 6 months ago by • 0
5
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7
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536
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how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
6 months ago pegah.taklifi ▴ 30
0
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1
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424
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DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 8 months ago by 58k • written 8 months ago by ▴ 240
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543
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
8 months ago • updated 4 months ago Rory Stark ★ 4.3k
2
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4
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376
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could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
8 months ago richardallenfriedmanbrooklyn • 0
0
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0
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371
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Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
10 months ago Goku • 0
2
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6
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416
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Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
10 months ago Goku • 0
0
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3
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338
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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 10 months ago by ▴ 160 • written 10 months ago by • 0
1
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4
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407
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DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
11 months ago • updated 10 months ago SFn • 0
0
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11
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699
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Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 11 months ago by • 0 • written 12 months ago by • 0
0
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2
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339
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DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
14 months ago • updated 13 months ago indi97 • 0
2
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2
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972
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ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
14 months ago • updated 12 months ago Mar Mar ▴ 20
1
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4
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1.1k
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MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 14 months ago by ★ 4.3k • written 4.0 years ago by • 0
2
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4
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763
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Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind Chipseq spike-ins
updated 14 months ago by ★ 4.3k • written 2.2 years ago by ▴ 30
4
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3
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350
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Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 14 months ago by ★ 4.3k • written 2.2 years ago by ▴ 10
1
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3
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1.5k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind chipseq chipqc
updated 14 months ago by ★ 4.3k • written 3.9 years ago by ▴ 10
1
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8
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782
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Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
15 months ago Hesh • 0
1
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1
reply
713
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 15 months ago by ★ 4.3k
0
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1
reply
311
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 15 months ago by 58k • written 15 months ago by • 0
0
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1
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334
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CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 21 months ago by 25k • written 21 months ago by ▴ 10
1
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7
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468
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DiffBind: dealing with replicates
diffbind chipseq
updated 22 months ago by ★ 4.3k • written 22 months ago by • 0
0
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1
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243
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Retrieving ChIP-seq data from Geo database
ChIPseq GEO data base
updated 23 months ago by 58k • written 23 months ago by • 0
0
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1
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234
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DiffBind MA plot annotate promoter regions with different colour
diffbind chipseq rorystark
updated 23 months ago by ★ 4.3k • written 23 months ago by ▴ 10
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0
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208
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How to change the text size for the names of ColAttributes
diffbind colattributes chipseq cex
2.2 years ago • updated 2.1 years ago researcher • 0
0
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0
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243
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ChIPQC makes a neverending loop while using all chromosomes
chipqc chipseq ChIPQC
2.4 years ago laura.mannarino ▴ 20
0
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1
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277
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diffBind analysis: only one replicate
diffbind chipseq
updated 2.4 years ago by ★ 4.3k • written 2.4 years ago by • 0
1
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3
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451
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Error: package or namespace load failed for 'ChIPseeker': 'TxDb.Hsapiens.UCSC.hg19.knownGene' is not exported from 'namespace: TxDb.Hsapiens.UCSC.hg1…
chipseq chipseeker R Bioconductor
updated 2.6 years ago by 25k • written 2.6 years ago by ▴ 10
0
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5
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432
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process bed/bedGraph files with the same coordinates for all the samples
ChIPSeq
2.6 years ago Kath • 0
2
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2
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1.1k
views
DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind R MAplot Chipseq
updated 2.7 years ago by ★ 4.3k • written 2.7 years ago by ▴ 10
0
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3
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402
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Diffbind affinity based analysis
Diffbind ChIPseq Affinity analysis Differentially bound sites occupancy analysis
updated 2.7 years ago by ★ 4.3k • written 2.7 years ago by • 0
0
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0
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688
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Error while annotating with Chipseeker
annotation chipseq
2.9 years ago hamaor • 0
0
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0
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589
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How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
3.1 years ago bioinfouser2 ▴ 10
3
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7
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1.7k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 3.1 years ago by 35k • written 3.1 years ago by • 0
3
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2
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632
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diffbind finding not differential site
diffbind chipseq histone chip-seq differential binding analysis
updated 3.2 years ago by ★ 4.3k • written 3.3 years ago by • 0
3
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4
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987
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ChIPseeker/Question about ''annoatePeak' function and for Bioconductor AnnotationData Packages for L.japonicus
chipseeker Bioconductor AnnotationData Packages Lotus japonicus ChIPseq
updated 3.3 years ago by 58k • written 3.3 years ago by • 0
0
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7
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644
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ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 3.4 years ago by ★ 1.3k • written 3.4 years ago by • 0
1
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3
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823
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How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 3.4 years ago by ★ 1.2k • written 3.5 years ago by ▴ 10
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0
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433
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Cannot open file because of connection error
systemArgs chipseq working directory
3.5 years ago hallie.s • 0
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0
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514
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Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
3.5 years ago l.brown ▴ 10
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0
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503
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Error when runing exomePeak
exomePeak chipseq
3.5 years ago syrttgump ▴ 20
0
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0
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406
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error in plotting data with CompareCluster function
comparecluster chipseq
3.5 years ago Ashley • 0
1
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1
reply
447
views
getting DiffBind full result list
deseq2 diffbind chipseq
updated 3.6 years ago by ★ 4.3k • written 3.6 years ago by • 0
2
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3
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1.0k
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind chipseq counts peaks bedtools
updated 8 months ago by ★ 4.3k • written 3.8 years ago by ▴ 10
0
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1
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474
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Reg.: Ringo,open source R package
agilent microarrays chipseq
updated 3.7 years ago by 58k • written 3.7 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: fgsea not downloading due to new r version. Is there a way around this? by amir.khan • 0
Seems to have done the trick and worked. thanks!
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Michael Love 35k
Just to underscore swbarnes2 advice above, I'd also recommend discussing statistical design with a local statistician or someone familiar w…
Answer: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
First, I'd start by looking at all your samples in PCA. Does sex have a strong effect? Does it make sense to compare one tissue with anot…
Comment: Unable to install Rhtslib in R-4.1.1 by cf2209 • 0
Thank you for your input I appreciate it. I will revise and make changes to this post as you suggested. Unfortunately I am not able to do t…
Comment: DiffBind dba.count Error in if (sum(tokeep) < length(tokeep)) by Rory Stark ★ 4.3k
I'm copying this over now, but have a couple of questions: 1. Did you create a `ScanBamParam`object, set `isUnmappedQuery`, and store it …
Votes
Answer: fgsea not downloading due to new r version. Is there a way around this?
Comment: Unable to install Rhtslib in R-4.1.1
Answer: fgsea not downloading due to new r version. Is there a way around this?
Answer: Swish with more than two conditions. Add support for contrasts?
Answer: ERROR: unable to find an inherited method for function ‘dispersions<-’ for signa
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