Showing : ChIPseq • reset
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14
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AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
17 hours ago Abhilansh • 0
0
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3
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79
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DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 2 days ago by ★ 4.4k • written 3 days ago by • 0
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0
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59
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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
18 days ago Swadha • 0
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1
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142
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Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 5 weeks ago by ★ 4.4k • written 9 weeks ago by • 0
1
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2
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183
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Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 8 weeks ago by ★ 4.4k • written 8 weeks ago by • 0
1
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1
reply
236
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DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 4 months ago by ★ 4.4k • written 5 months ago by • 0
0
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0
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140
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
5 months ago Nadav • 0
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0
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179
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
7 months ago Drew • 0
0
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6
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452
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cel files with affy library
ChIPSeq
updated 9 months ago by • 0 • written 9 months ago by • 0
3
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12
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1.0k
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Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 9 months ago by ★ 4.4k • written 2.7 years ago by ▴ 20
0
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2
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330
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Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
9 months ago maria.soler • 0
2
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3
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414
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An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 8 months ago by ▴ 20 • written 9 months ago by • 0
5
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7
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647
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how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 6 weeks ago by • 0 • written 10 months ago by ▴ 30
0
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1
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569
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DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 11 months ago by 59k • written 11 months ago by ▴ 250
1
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2
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733
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
11 months ago • updated 8 months ago Rory Stark ★ 4.4k
2
votes
4
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434
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could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
12 months ago • updated 11 months ago richardallenfriedmanbrooklyn • 0
0
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0
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499
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Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
13 months ago Goku • 0
2
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6
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479
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Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
13 months ago Goku • 0
0
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3
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395
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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 14 months ago by ▴ 280 • written 14 months ago by • 0
1
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4
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466
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DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
15 months ago • updated 14 months ago SFn • 0
0
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11
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802
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Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 15 months ago by • 0 • written 16 months ago by • 0
0
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2
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383
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DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
17 months ago indi97 • 0
2
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2
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1.2k
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ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
18 months ago • updated 15 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 18 months ago by ★ 4.4k • written 4.3 years ago by • 0
2
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4
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907
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Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind Chipseq spike-ins
updated 18 months ago by ★ 4.4k • written 2.5 years ago by ▴ 30
4
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3
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388
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 18 months ago by ★ 4.4k • written 2.5 years ago by ▴ 10
1
vote
3
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1.6k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind chipseq chipqc
updated 18 months ago by ★ 4.4k • written 4.2 years ago by ▴ 10
1
vote
8
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939
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Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
18 months ago Hesh • 0
1
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1
reply
817
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News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 18 months ago by ★ 4.4k
0
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1
reply
429
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 18 months ago by 59k • written 18 months ago by • 0
0
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1
reply
403
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 2.1 years ago by 25k • written 2.1 years ago by ▴ 10
1
vote
7
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653
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DiffBind: dealing with replicates
diffbind chipseq
updated 2.2 years ago by ★ 4.4k • written 2.2 years ago by • 0
0
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1
reply
298
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Retrieving ChIP-seq data from Geo database
ChIPseq GEO data base
updated 2.2 years ago by 59k • written 2.2 years ago by • 0
0
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1
reply
271
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DiffBind MA plot annotate promoter regions with different colour
diffbind chipseq rorystark
updated 2.2 years ago by ★ 4.4k • written 2.3 years ago by ▴ 10
0
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0
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233
views
How to change the text size for the names of ColAttributes
diffbind colattributes chipseq cex
2.5 years ago • updated 2.4 years ago researcher • 0
0
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0
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276
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ChIPQC makes a neverending loop while using all chromosomes
chipqc chipseq ChIPQC
2.7 years ago laura.mannarino ▴ 20
0
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1
reply
326
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diffBind analysis: only one replicate
diffbind chipseq
updated 2.7 years ago by ★ 4.4k • written 2.7 years ago by • 0
1
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3
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494
views
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 2.9 years ago by 25k • written 2.9 years ago by ▴ 10
0
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5
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490
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process bed/bedGraph files with the same coordinates for all the samples
ChIPSeq
2.9 years ago Kath • 0
2
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2
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1.2k
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DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind R MAplot Chipseq
updated 3.0 years ago by ★ 4.4k • written 3.0 years ago by ▴ 10
0
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3
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436
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Diffbind affinity based analysis
Diffbind ChIPseq Affinity analysis Differentially bound sites occupancy analysis
updated 3.0 years ago by ★ 4.4k • written 3.0 years ago by • 0
0
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0
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719
views
Error while annotating with Chipseeker
annotation chipseq
3.2 years ago hamaor • 0
0
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0
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633
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How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
3.4 years ago bioinfouser2 ▴ 10
3
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7
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1.8k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 3.4 years ago by 36k • written 3.4 years ago by • 0
3
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2
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663
views
diffbind finding not differential site
diffbind chipseq histone chip-seq differential binding analysis
updated 3.5 years ago by ★ 4.4k • written 3.6 years ago by • 0
3
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4
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1.1k
views
ChIPseeker/Question about ''annoatePeak' function and for Bioconductor AnnotationData Packages for L.japonicus
chipseeker Bioconductor AnnotationData Packages Lotus japonicus ChIPseq
updated 3.6 years ago by 59k • written 3.6 years ago by • 0
0
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7
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689
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ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 3.7 years ago by ★ 1.3k • written 3.7 years ago by • 0
1
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3
replies
880
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How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 3.7 years ago by ★ 1.2k • written 3.8 years ago by ▴ 10
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0
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462
views
Cannot open file because of connection error
systemArgs chipseq working directory
3.8 years ago hallie.s • 0
0
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0
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549
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
3.8 years ago l.brown ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by karenserrano • 0
Hi Johannes, Could I request the same EnsDb creation for Medicago truncatula? Thank you very much, Karen
Answer: EnrichGO not working with db created from annotationhub by Guido Hooiveld ★ 3.2k
Did you notice the first message that was returned after you ran `enrichGO()`? Thus: `--> No gene can be mapped....` This basically means…
Comment: DiffBind GreyListChIP error: Error: BiocParallel errors by ksong • 0
Hello my friends, I have exactly the same issue. May I ask if you have already solve this problem? I have tried `library(BiocParallel) regi…
Comment: cellCounts() function floating point error by Wei Shi ★ 3.3k
Yes we are currently working on generating a small example for cellCounts.
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU by ksong • 0
Hi Dr Sudbery, yes I found looking at the coverage in IGV helps a lot. I did find some differences between CDS and UTR and between samples.…
Votes
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
C: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o
Comment: Diffbind dba$binding slot finding Chr21 for an MM10 dataset
Answer: Handling NA values in limma's voom design matrix
Answer: Handling NA values in limma's voom design matrix
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