Showing : ChIPseeker • reset
7
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11
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4.9k
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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 6.4 years ago by ★ 1.2k • written 6.4 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
993
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
893
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
replies
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
14 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
984
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
970
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
2.6k
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
682
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: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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