Showing : ChiPseeker • reset
7
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4.8k
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annotatePeak() in ChIPseeker - how long does it take to run?
annotatePeak chipseeker chipseq org.Mm.eg.db TxDb.Mmusculus.UCSC.mm9.knownGene
updated 8.6 years ago by 25k • written 8.8 years ago by • 0
1
vote
11
replies
2.8k
views
ChIPseeker question: provide custom csAnno to plots
chipseeker
8.5 years ago francesca casalino ▴ 50
3
votes
10
replies
4.5k
views
ChIPseeker question: enrichPeakOverlap to find enrichment of genomic annotations in peaks from GRanges
chipseeker
updated 8.5 years ago by ★ 1.2k • written 8.6 years ago by ▴ 50
1
vote
9
replies
3.8k
views
Question about ChiPseeker: plot other values in plotAvgProf2
ChiPseeker
updated 8.5 years ago by ★ 1.2k • written 8.6 years ago by ▴ 50
0
votes
8
replies
2.0k
views
significance of ChIPseq peak overlap
chipseeker
updated 7.8 years ago by ★ 1.2k • written 7.8 years ago by ▴ 10
5
votes
7
replies
2.2k
views
ChIPSeeker enrichPeakOverlap external dataset downloads
chipseeker chipseq chip
updated 6.3 years ago by ★ 1.2k • written 6.3 years ago by ▴ 60
3
votes
6
replies
1.6k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
5.8 years ago 94133 • 0
0
votes
6
replies
2.3k
views
Chipseeker is unavabile on Linux CentOS7 ?
Bioconduct or Chipseeker CentOS7 Linux installation
updated 7.5 years ago by ★ 1.2k • written 7.5 years ago by • 0
2
votes
6
replies
2.5k
views
ChIPseeker: covplot function: error with some ENCODE data sets
chiPseeker covplot ENCODE ChIpseq
9.0 years ago sarabusquets88 • 0
1
vote
4
replies
2.0k
views
Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
3.2 years ago Kasit • 0
2
votes
4
replies
1.2k
views
Quantifying peaks corresponding to a purticular feature
chipseeker
8.9 years ago snigdhapola • 0
1
vote
4
replies
2.1k
views
ChIPseeker: Is it possible to create heatmaps / metagene plots without being centered on the TSS?
chipseq chipseeker exon start site
updated 8.6 years ago by ★ 1.2k • written 8.6 years ago by • 0
3
votes
4
replies
2.0k
views
ChIPseeker::vennplot() fails with Error in ss[[1]] : subscript out of bounds
chipseeker venn vennplot genomicranges granges
7.8 years ago enricoferrero ▴ 660
3
votes
4
replies
2.4k
views
ChIPseeker/Question about ''annoatePeak' function and for Bioconductor AnnotationData Packages for L.japonicus
chipseeker Bioconductor AnnotationData Packages Lotus japonicus ChIPseq
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
1
vote
3
replies
1.1k
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 4.8 years ago by 25k • written 4.8 years ago by ▴ 10
0
votes
3
replies
1.9k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
6.3 years ago andrew.gehrke • 0
0
votes
3
replies
2.0k
views
"input object should be a named list" error in ChIPseeker
ChIPseeker named list error plotAnnoBar plotDistToTSS vennplot
updated 6.1 years ago by ★ 1.2k • written 6.1 years ago by • 0
1
vote
3
replies
1.5k
views
How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 5.6 years ago by ★ 1.2k • written 5.7 years ago by ▴ 10
5
votes
3
replies
1.3k
views
importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 3.5 years ago by 65k • written 3.5 years ago by ▴ 10
0
votes
3
replies
991
views
ChIPseeker read count calculation
chipseeker plotAvgProf
updated 7.6 years ago by ★ 1.2k • written 7.6 years ago by • 0
0
votes
3
replies
2.0k
views
Chipseeker : problem running Chipseeker to ENCODE datasets
chipseeker
updated 9.0 years ago by ★ 1.2k • written 9.0 years ago by • 0
1
vote
3
replies
1.4k
views
ChIPseeker Error: Attempting to annotatePeaks
ChIPseeker software error
updated 8.6 years ago by ★ 1.2k • written 8.6 years ago by • 0
2
votes
3
replies
2.6k
views
ChIPseeker peak annotation tssRegion
chipseeker annotation chipseq
6.5 years ago lifeng.liu.biology ▴ 10
1
vote
3
replies
889
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
2.9 years ago Meghna • 0
1
vote
2
replies
3.7k
views
Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
4.6 years ago researcher • 0
0
votes
2
replies
1.2k
views
how to get frequencies from plotDistToTSS
chipseeker
5.4 years ago KKO • 0
0
votes
2
replies
1.2k
views
What is the confidence interval in ChIPseeker::plotAvgProf?
chipseeker
7.1 years ago enricoferrero ▴ 660
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
0
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2
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1.4k
views
Annotation within ChIPSeeker mismatch geneId and annotation column
ChIPseeker
8.5 years ago n.kreim ▴ 20
0
votes
2
replies
3.2k
views
Cannot install packages in R/BiocManager_Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TR…
Bioconductor BioCManager ChIPseeker
updated 16 months ago by 65k • written 16 months ago by • 0
1
vote
2
replies
1.0k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
13 months ago chavaleab • 0
0
votes
2
replies
2.4k
views
ChIPseeker annotatePeak definition
chipseeker
updated 7.7 years ago by ★ 1.2k • written 7.7 years ago by ▴ 140
0
votes
2
replies
1.0k
views
ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
3.1 years ago Onur Karakaslar • 0
0
votes
2
replies
978
views
getPromoters
ChIPseeker
2.5 years ago guoyou88 • 0
0
votes
2
replies
2.6k
views
custom annotation in annotatePeak
chipseeker Guangchuang Yu
6.3 years ago andrew.gehrke • 0
3
votes
2
replies
1.7k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 5.2 years ago by ★ 2.0k • written 5.2 years ago by ▴ 100
0
votes
1
reply
969
views
ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
23 months ago Gyan Prakash Mishra ▴ 10
0
votes
1
reply
1.6k
views
ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
4.1 years ago Assa Yeroslaviz ★ 1.5k
0
votes
1
reply
3.1k
views
ChIPseeker: Error in annotatePeak
Sequencing GO annotate ChIPseeker Sequencing GO annotate ChIPseeker
10.0 years ago António Miguel de Jesus Domingues ▴ 510
0
votes
1
reply
1.3k
views
[ChIPseeker; feature request] More flexibility in specifying the TSS region
ChIPseeker featurerequest tss
updated 8.2 years ago by ★ 1.2k • written 8.2 years ago by ▴ 40
0
votes
1
reply
1.5k
views
ChIPseeker gene body plot
chipseeker visualization
updated 7.9 years ago by ★ 1.2k • written 7.9 years ago by ▴ 40
0
votes
1
reply
1.6k
views
ChIPseeker, read multiple peak files
chipseeker
updated 7.5 years ago by 65k • written 7.6 years ago by • 0
0
votes
1
reply
1.3k
views
How to show the fraction of peaks in CDS regions using ChIPseeker
chipseeker
updated 7.5 years ago by ★ 1.2k • written 7.5 years ago by • 0
0
votes
1
reply
1.3k
views
ChIPseeker : definition of each genomic location in annotatepeak
chipseeker
updated 7.4 years ago by ★ 1.2k • written 7.4 years ago by • 0
0
votes
1
reply
1.8k
views
ChIPseeker TSS plot
chipseeker plotAvgProf
updated 7.2 years ago by ★ 1.2k • written 7.3 years ago by • 0
0
votes
1
reply
1.5k
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 6.9 years ago by ★ 1.2k • written 6.9 years ago by • 0
2
votes
1
reply
2.5k
views
ChIPseeker mapping between keys and columns
chipseeker chipseq
updated 6.6 years ago by ▴ 680 • written 6.6 years ago by ▴ 60
3
votes
1
reply
1.3k
views
chipseeker annotation of focused genic regions
chipseeker annotatepeak
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by • 0
0
votes
1
reply
2.2k
views
how to define the downstream range in ChIPseeker
ChIPseeker H3K27me3 chipseq chipseeker
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by ▴ 10
0
votes
1
reply
681
views
Error in getGenomicAnnoStat(peak.gr) : object 'plab' not found
ChIPseeker
updated 6.1 years ago by ★ 1.2k • written 6.1 years ago by • 0
50 results • Page 1 of 1
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Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM() by James W. MacDonald 65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
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Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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Scholar to Rory Stark ★ 5.2k
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