Showing : ChIPSeq • reset
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Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
updated 3 days ago by 43k • written 3 days ago by • 0
1
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2
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132
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An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
5 days ago • updated 2 days ago zhuyi05 • 0
5
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7
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246
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how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
15 days ago • updated 11 days ago pegah.taklifi ▴ 30
0
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1
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127
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DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 9 weeks ago by 57k • written 9 weeks ago by ▴ 240
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144
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
9 weeks ago Rory Stark ★ 4.0k
2
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4
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226
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could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
11 weeks ago • updated 8 weeks ago richardallenfriedmanbrooklyn • 0
0
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4
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370
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Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 12 weeks ago by ★ 4.0k • written 22 months ago by ▴ 20
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0
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138
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Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
4 months ago Goku • 0
2
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6
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278
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Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
4 months ago Goku • 0
0
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3
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202
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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 4 months ago by ▴ 150 • written 4 months ago by • 0
1
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4
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252
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DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
5 months ago • updated 4 months ago SFn • 0
0
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11
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479
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Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 5 months ago by • 0 • written 6 months ago by • 0
0
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2
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247
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DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
8 months ago • updated 7 months ago indi97 • 0
0
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2
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531
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ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
8 months ago • updated 5 months ago Mar Mar • 0
1
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4
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917
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MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 8 months ago by ★ 4.0k • written 3.5 years ago by • 0
2
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4
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461
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Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind Chipseq spike-ins
updated 8 months ago by ★ 4.0k • written 20 months ago by ▴ 20
4
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3
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247
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Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 8 months ago by ★ 4.0k • written 21 months ago by ▴ 10
1
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3
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1.2k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind chipseq chipqc
updated 8 months ago by ★ 4.0k • written 3.4 years ago by ▴ 10
1
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8
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487
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Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
9 months ago Hesh • 0
1
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1
reply
480
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 9 months ago by ★ 4.0k
0
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1
reply
156
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 9 months ago by 57k • written 9 months ago by • 0
0
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1
reply
208
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CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 15 months ago by 25k • written 15 months ago by ▴ 10
1
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7
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207
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DiffBind: dealing with replicates
diffbind chipseq
updated 16 months ago by ★ 4.0k • written 16 months ago by • 0
0
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1
reply
157
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Retrieving ChIP-seq data from Geo database
ChIPseq GEO data base
updated 17 months ago by 57k • written 17 months ago by • 0
0
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1
reply
137
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DiffBind MA plot annotate promoter regions with different colour
diffbind chipseq rorystark
updated 17 months ago by ★ 4.0k • written 17 months ago by ▴ 10
0
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0
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142
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How to change the text size for the names of ColAttributes
diffbind colattributes chipseq cex
20 months ago researcher • 0
0
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0
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177
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ChIPQC makes a neverending loop while using all chromosomes
chipqc chipseq ChIPQC
22 months ago laura.mannarino ▴ 20
0
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1
reply
186
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diffBind analysis: only one replicate
diffbind chipseq
updated 23 months ago by ★ 4.0k • written 23 months ago by • 0
1
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3
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365
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 2.1 years ago by 25k • written 2.1 years ago by ▴ 10
0
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5
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315
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process bed/bedGraph files with the same coordinates for all the samples
ChIPSeq
2.1 years ago Kath • 0
2
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2
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837
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DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind R MAplot Chipseq
updated 2.2 years ago by ★ 4.0k • written 2.2 years ago by ▴ 10
0
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3
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313
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Diffbind affinity based analysis
Diffbind ChIPseq Affinity analysis Differentially bound sites occupancy analysis
updated 2.2 years ago by ★ 4.0k • written 2.2 years ago by • 0
0
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0
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592
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Error while annotating with Chipseeker
annotation chipseq
2.4 years ago hamaor • 0
0
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0
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470
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How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
2.6 years ago bioinfouser2 ▴ 10
3
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7
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1.3k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 2.6 years ago by 33k • written 2.6 years ago by • 0
3
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2
replies
478
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diffbind finding not differential site
diffbind chipseq histone chip-seq differential binding analysis
updated 2.8 years ago by ★ 4.0k • written 2.8 years ago by • 0
3
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4
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765
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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 2.8 years ago by 57k • written 2.8 years ago by • 0
0
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7
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540
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ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 2.9 years ago by ★ 1.2k • written 2.9 years ago by • 0
1
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3
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689
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How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 2.9 years ago by ★ 1.2k • written 3.0 years ago by ▴ 10
0
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0
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349
views
Cannot open file because of connection error
systemArgs chipseq working directory
3.0 years ago hallie.s • 0
0
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0
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426
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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
3.0 years ago l.brown ▴ 10
0
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0
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430
views
Error when runing exomePeak
exomePeak chipseq
3.0 years ago syrttgump ▴ 20
0
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0
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334
views
error in plotting data with CompareCluster function
comparecluster chipseq
3.0 years ago Ashley • 0
1
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1
reply
387
views
getting DiffBind full result list
deseq2 diffbind chipseq
updated 3.2 years ago by ★ 4.0k • written 3.2 years ago by • 0
2
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3
replies
794
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Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind chipseq counts peaks bedtools
updated 12 weeks ago by ★ 4.0k • written 3.3 years ago by ▴ 10
0
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1
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403
views
Reg.: Ringo,open source R package
agilent microarrays chipseq
updated 3.2 years ago by 57k • written 3.2 years ago by • 0
4
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7
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1.3k
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Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 3.2 years ago by 33k • written 3.2 years ago by ▴ 20
0
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417
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Differential ChIP regions across >2 conditions
diffbind chipseq
3.3 years ago Shamaine • 0
2
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3
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2.1k
views
Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
diffbind chipseq peaks dba is.na
3.3 years ago maria.kondili • 0
1
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1
reply
510
views
enrichGO (clusterProfiler) produces different results
chipseq go enrichment clusterprofiler
updated 3.4 years ago by ★ 1.2k • written 3.4 years ago by ▴ 840
50 results • Page 1 of 1
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Comment: featureCounts - paired-end data by Yanfang • 0
Hey Wei shi, May I ask you something related to featureCounts? I have only paired end reads (RNAseq) mapping to its genome by bowtie2, an…
Comment: WGCNA adjust p value by Kevin Blighe 3.2k
Cross-posted: https://www.biostars.org/p/9482927/
Comment: Unique GPos taking into account mcols by Marcel Ramos 540
Hi @maltethodberg We currently do not have a method that does this. Perhaps a `duplicated` method is appropriate but I am not the develop…
Comment: What are these genes ? [How to get Ensembl IDs for them] by abf ▴ 30
Mouse genes are not typically all capitals, but I was able to find a reference to a mouse gene in NCBI to [CH36-217G15][1]. Maybe this is …
Comment: Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db. by abf ▴ 30
I should note that when I query org.Mm.eg.db using the gene Symbols associated with my differential expression data I find a 1:1 correspond…
Votes
A: Normalized counts of DESeq2 affected by design formula?
A: Finding orthologous human/mouse ENSEMBL IDs
Comment: What are these genes ? [How to get Ensembl IDs for them]
Answer: What lfcSE is dependent upon?
Comment: P value and Adj. P value showing N/A
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