Showing : ChIPseq • reset
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73
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could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
updated 3 days ago by ★ 26k • written 5 days ago by • 0
0
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4
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258
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Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 10 days ago by ★ 3.9k • written 20 months ago by ▴ 20
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0
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69
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Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
7 weeks ago Goku • 0
2
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6
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197
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Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
8 weeks ago • updated 7 weeks ago Goku • 0
0
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3
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137
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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 9 weeks ago by ▴ 80 • written 9 weeks ago by • 0
1
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4
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186
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DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
3 months ago • updated 10 weeks ago SFn • 0
0
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11
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356
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Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 3 months ago by • 0 • written 4 months ago by • 0
0
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2
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191
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DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
5 months ago indi97 • 0
0
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2
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349
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ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
6 months ago • updated 3 months ago Mar Mar • 0
1
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4
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850
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MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 6 months ago by ★ 3.9k • written 3.3 years ago by • 0
2
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4
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350
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Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind Chipseq spike-ins
updated 6 months ago by ★ 3.9k • written 18 months ago by ▴ 20
4
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3
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193
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Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 6 months ago by ★ 3.9k • written 18 months ago by ▴ 10
1
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3
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1.1k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind chipseq chipqc
updated 6 months ago by ★ 3.9k • written 3.2 years ago by ▴ 10
1
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8
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378
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Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
6 months ago Hesh • 0
1
vote
1
reply
349
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 6 months ago by ★ 3.9k
0
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1
reply
93
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 6 months ago by 56k • written 6 months ago by • 0
0
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1
reply
151
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CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 13 months ago by 25k • written 13 months ago by ▴ 10
1
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7
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132
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DiffBind: dealing with replicates
diffbind chipseq
updated 14 months ago by ★ 3.9k • written 14 months ago by • 0
0
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1
reply
106
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Retrieving ChIP-seq data from Geo database
ChIPseq GEO data base
updated 15 months ago by 56k • written 15 months ago by • 0
0
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1
reply
94
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DiffBind MA plot annotate promoter regions with different colour
diffbind chipseq rorystark
updated 15 months ago by ★ 3.9k • written 15 months ago by ▴ 10
0
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0
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114
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How to change the text size for the names of ColAttributes
diffbind colattributes chipseq cex
18 months ago • updated 17 months ago researcher • 0
0
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0
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144
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ChIPQC makes a neverending loop while using all chromosomes
chipqc chipseq ChIPQC
20 months ago laura.mannarino ▴ 20
0
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1
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155
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diffBind analysis: only one replicate
diffbind chipseq
updated 20 months ago by ★ 3.9k • written 20 months ago by • 0
1
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3
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316
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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 22 months ago by 25k • written 22 months ago by ▴ 10
0
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5
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260
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process bed/bedGraph files with the same coordinates for all the samples
ChIPSeq
23 months ago Kath • 0
2
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2
replies
710
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DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind R MAplot Chipseq
updated 23 months ago by ★ 3.9k • written 23 months ago by ▴ 10
0
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3
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240
views
Diffbind affinity based analysis
Diffbind ChIPseq Affinity analysis Differentially bound sites occupancy analysis
updated 24 months ago by ★ 3.9k • written 24 months ago by • 0
0
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0
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545
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Error while annotating with Chipseeker
annotation chipseq
2.2 years ago hamaor • 0
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0
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402
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How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
2.4 years ago bioinfouser2 ▴ 10
3
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7
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1.1k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 2.4 years ago by 33k • written 2.4 years ago by • 0
3
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2
replies
425
views
diffbind finding not differential site
diffbind chipseq histone chip-seq differential binding analysis
updated 2.5 years ago by ★ 3.9k • written 2.6 years ago by • 0
3
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4
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677
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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 2.6 years ago by 56k • written 2.6 years ago by • 0
0
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7
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469
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ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 2.7 years ago by ★ 1.2k • written 2.7 years ago by • 0
1
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3
replies
637
views
How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 2.7 years ago by ★ 1.2k • written 2.8 years ago by ▴ 10
0
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0
replies
315
views
Cannot open file because of connection error
systemArgs chipseq working directory
2.8 years ago hallie.s • 0
0
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0
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389
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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
2.8 years ago l.brown ▴ 10
0
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0
replies
389
views
Error when runing exomePeak
exomePeak chipseq
2.8 years ago syrttgump ▴ 20
0
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0
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305
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error in plotting data with CompareCluster function
comparecluster chipseq
2.8 years ago Ashley • 0
1
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1
reply
351
views
getting DiffBind full result list
deseq2 diffbind chipseq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
2
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3
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693
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind chipseq counts peaks bedtools
updated 10 days ago by ★ 3.9k • written 3.1 years ago by ▴ 10
0
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1
reply
375
views
Reg.: Ringo,open source R package
agilent microarrays chipseq
updated 3.0 years ago by 56k • written 3.0 years ago by • 0
4
votes
7
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1.2k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 3.0 years ago by 33k • written 3.0 years ago by ▴ 20
0
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0
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383
views
Differential ChIP regions across >2 conditions
diffbind chipseq
3.1 years ago Shamaine • 0
2
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3
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2.0k
views
Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
diffbind chipseq peaks dba is.na
3.1 years ago maria.kondili • 0
1
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1
reply
467
views
enrichGO (clusterProfiler) produces different results
chipseq go enrichment clusterprofiler
updated 3.2 years ago by ★ 1.2k • written 3.2 years ago by ▴ 840
2
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4
replies
731
views
Make window around TSS and get values from another data.frame for bins of the specified window
R granges genomicranges chipseq
updated 3.3 years ago by 11k • written 3.4 years ago by ▴ 20
1
vote
1
reply
400
views
Filtering a BED file according to genomic annotation
bed files bedtools filtering chipseq
updated 3.4 years ago by ★ 26k • written 3.4 years ago by ▴ 60
5
votes
7
replies
836
views
ChIPSeeker enrichPeakOverlap external dataset downloads
chipseeker chipseq chip
updated 3.4 years ago by ★ 1.2k • written 3.4 years ago by ▴ 60
4
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3
replies
569
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 3.4 years ago by ★ 26k • written 3.4 years ago by ▴ 60
0
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0
replies
559
views
Job: Bioinformatics Analyst II/III - Banchereau Lab @ The Jackson Laboratory
rnaseq atac-seq iso-seq chipseq Job
3.4 years ago tyler.chukwu • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: `aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size awa by Koki • 0
Ok, I got the gist of it. If I have the same situation of the previous case (https://support.bioconductor.org/p/9136736/), where I have to…
Answer: DESeq2 Design matrix by Michael Love 33k
Usually one would use a single design and extract comparisons. With a complex design, you should partner with someone familiar with linear …
Comment: `aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size awa by Hervé Pagès 14k
> For example, the following codes use a combination of delayed operation and block-processed operation but the code as a whole does not ex…
Answer: Technical reps by Michael Love 33k
I would go back and attempt to map but allowing a higher insert size. I think a number of RNA-seq alignment tools have this as an option. I…
Comment: ASpli: jCounts() Error in av[at] <- a[at] : NAs are not allowed in subscripted a by Emma ▴ 10
Hi Estefi, I tried to do the devel version install, but it requires R 4.1, which I don't have on my cluster. It's not possible for me to …
Votes
Comment: `aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size awa
Answer: Error: C stack usage of HDF5Array
Answer: "dim<-" against on-disk arrays
Answer: `aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size awa
Answer: ASpli: jCounts() Error in av[at] <- a[at] : NAs are not allowed in subscripted a
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