Showing : ChIPseeker • reset
7
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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
5
votes
7
replies
2.2k
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ChIPSeeker enrichPeakOverlap external dataset downloads
chipseeker chipseq chip
updated 6.4 years ago by ★ 1.2k • written 6.4 years ago by ▴ 60
5
votes
3
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1.4k
views
importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 3.5 years ago by 65k • written 3.5 years ago by ▴ 10
3
votes
2
replies
1.8k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 5.2 years ago by ★ 2.0k • written 5.3 years ago by ▴ 100
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
3
votes
4
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2.5k
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
3
votes
10
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4.5k
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ChIPseeker question: enrichPeakOverlap to find enrichment of genomic annotations in peaks from GRanges
chipseeker
updated 8.6 years ago by ★ 1.2k • written 8.6 years ago by ▴ 50
3
votes
4
replies
2.0k
views
ChIPseeker::vennplot() fails with Error in ss[[1]] : subscript out of bounds
chipseeker venn vennplot genomicranges granges
7.9 years ago enricoferrero ▴ 660
3
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6
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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
2
votes
6
replies
2.5k
views
ChIPseeker: covplot function: error with some ENCODE data sets
chiPseeker covplot ENCODE ChIpseq
9.1 years ago sarabusquets88 • 0
2
votes
2
replies
2.4k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
3.5 years ago • updated 3.3 years ago Mar Mar ▴ 20
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
2
votes
3
replies
2.6k
views
ChIPseeker peak annotation tssRegion
chipseeker annotation chipseq
6.5 years ago lifeng.liu.biology ▴ 10
2
votes
1
reply
3.6k
views
Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
4.7 years ago endrebak85 ▴ 40
2
votes
4
replies
1.2k
views
Quantifying peaks corresponding to a purticular feature
chipseeker
8.9 years ago snigdhapola • 0
1
vote
1
reply
1.7k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 2.8 years ago by • 0 • written 5.4 years ago by ▴ 10
1
vote
3
replies
1.2k
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 4.9 years ago by 25k • written 4.9 years ago by ▴ 10
1
vote
2
replies
1.1k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
14 months ago chavaleab • 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
4.7 years ago researcher • 0
1
vote
11
replies
2.8k
views
ChIPseeker question: provide custom csAnno to plots
chipseeker
8.6 years ago francesca casalino ▴ 50
1
vote
0
replies
650
views
Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
21 months ago arisarkar88 ▴ 40
1
vote
0
replies
1.0k
views
ChipSeeker Flanking gene annotation
chipseeker
5.6 years ago Lauma R ▴ 10
1
vote
0
replies
889
views
Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
4.0 years ago egbastakis • 0
1
vote
1
reply
2.1k
views
Error: package or namespace load failed for 'ChIPseeker' in dyn.load(file, DLLpath = DLLpath
chipseeker
5.9 years ago liucz200904 • 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
1
vote
3
replies
1.5k
views
ChIPseeker Error: Attempting to annotatePeaks
ChIPseeker software error
updated 8.6 years ago by ★ 1.2k • written 8.6 years ago by • 0
1
vote
3
replies
1.6k
views
How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 5.7 years ago by ★ 1.2k • written 5.8 years ago by ▴ 10
1
vote
9
replies
3.8k
views
Question about ChiPseeker: plot other values in plotAvgProf2
ChiPseeker
updated 8.6 years ago by ★ 1.2k • written 8.6 years ago by ▴ 50
1
vote
3
replies
898
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
2.9 years ago Meghna • 0
1
vote
4
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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
0
votes
2
replies
1.2k
views
how to get frequencies from plotDistToTSS
chipseeker
5.4 years ago KKO • 0
0
votes
0
replies
1.1k
views
How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
5.4 years ago bioinfouser2 ▴ 10
0
votes
1
reply
1.1k
views
Problem in using covplot ChIPseeker
ChIPseeker software error
5.2 years ago vasudha.sharma • 0
0
votes
1
reply
2.6k
views
error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
5.0 years ago Theo ▴ 10
0
votes
1
reply
1.6k
views
Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
4.6 years ago sutturka • 0
0
votes
1
reply
1.0k
views
ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
4.2 years ago Guandong Shang ▴ 40
0
votes
0
replies
749
views
Potential oversimplification in the overlap function
ChIPseeker
4.0 years ago konsta.kukkonen • 0
0
votes
0
replies
868
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
4.0 years ago hfyuan2016 • 0
0
votes
1
reply
901
views
p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 9 months ago by • 0 • written 3.8 years ago by • 0
0
votes
1
reply
1.8k
views
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
3.7 years ago amafon95 • 0
0
votes
0
replies
771
views
How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
3.6 years ago bioinfouser2 ▴ 10
0
votes
0
replies
905
views
About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
3.6 years ago ahua217 ▴ 10
0
votes
1
reply
1.5k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 3.6 years ago by 65k • written 3.6 years ago by • 0
0
votes
0
replies
636
views
Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
3.5 years ago Prasoon • 0
0
votes
0
replies
748
views
Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
3.5 years ago Sam ▴ 10
0
votes
0
replies
693
views
ChIPSeeker covplot function, fix yaxis
ChIPseeker
3.3 years ago jordi.planells • 0
0
votes
0
replies
35
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
18 hours ago Anton01 • 0
0
votes
2
replies
1.0k
views
ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
3.2 years ago Onur Karakaslar • 0
0
votes
0
replies
1.1k
views
Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
3.1 years ago Xiaojie Cheng • 0
0
votes
0
replies
718
views
What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
2.1 years ago hyjforesight • 0
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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