Showing : ChIPseeker • reset
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ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
2 days ago • updated 3 hours ago Gyan Prakash Mishra • 0
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62
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Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
23 days ago Swadha • 0
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63
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What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
7 weeks ago hyjforesight • 0
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1
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509
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ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
6 months ago william.ho • 0
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2
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291
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getPromoters
ChIPseeker
7 months ago guoyou88 • 0
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227
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ChIPseeker, how to customize plotDistToTSS
ChIPseeker
7 months ago alexandre.blais ▴ 50
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3
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282
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what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
11 months ago • updated 10 months ago Meghna • 0
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225
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CHIPseeker- promoter gene names
ChIPseeker CHIPsee
11 months ago rb • 0
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1
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327
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ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 13 months ago by ▴ 10 • written 13 months ago by • 0
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225
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What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
13 months ago Sam ▴ 10
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307
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Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
13 months ago Xiaojie Cheng • 0
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2
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462
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ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
14 months ago Onur Karakaslar • 0
1
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4
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507
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Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
15 months ago Kasit • 0
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195
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ChIPSeeker covplot function, fix yaxis
ChIPseeker
16 months ago jordi.planells • 0
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251
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Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
18 months ago • updated 17 months ago Sam ▴ 10
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2
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1.2k
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ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
18 months ago • updated 15 months ago Mar Mar ▴ 20
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428
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importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 18 months ago by 59k • written 18 months ago by • 0
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194
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Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
18 months ago Prasoon • 0
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1
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433
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How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 18 months ago by 59k • written 18 months ago by • 0
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332
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About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
19 months ago ahua217 ▴ 10
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320
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How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
19 months ago bioinfouser2 ▴ 10
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1
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599
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ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
20 months ago amafon95 • 0
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294
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p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
21 months ago mwong043 • 0
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350
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ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
2.0 years ago hfyuan2016 • 0
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267
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Potential oversimplification in the overlap function
ChIPseeker
2.0 years ago konsta.kukkonen • 0
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311
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Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
2.0 years ago egbastakis • 0
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1
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652
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ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
2.1 years ago Assa Yeroslaviz ★ 1.5k
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1
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403
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ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
2.3 years ago Guandong Shang ▴ 20
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1
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564
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Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
2.7 years ago sutturka • 0
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2.4k
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Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
2.7 years ago researcher • 0
2
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1
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1.2k
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Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
2.7 years ago endrebak85 ▴ 30
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3
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497
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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 2.9 years ago by 25k • written 2.9 years ago by ▴ 10
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1.2k
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error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
3.0 years ago theodore.georgomanolis • 0
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1
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558
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Problem in using covplot ChIPseeker
ChIPseeker software error
3.2 years ago vasudha.sharma • 0
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2
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864
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How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 3.3 years ago by ★ 1.9k • written 3.3 years ago by ▴ 80
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1
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849
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 10 months ago by • 0 • written 3.4 years ago by ▴ 10
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636
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How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
3.4 years ago bioinfouser2 ▴ 10
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2
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648
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how to get frequencies from plotDistToTSS
chipseeker
3.4 years ago KKO • 0
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522
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ChipSeeker Flanking gene annotation
chipseeker
3.6 years ago Lauma R ▴ 10
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4
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1.1k
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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 3.6 years ago by 59k • written 3.6 years ago by • 0
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437
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covplot and getChrCov function
chipseeker
3.6 years ago xiaofeiwang198266 • 0
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3
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882
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How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 3.7 years ago by ★ 1.2k • written 3.8 years ago by ▴ 10
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452
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How to get the genome distribution in proportion of promoter, 1st exon, other exon, 1st intron, other intron, distal intergenic, etc from a species
chipseeker
3.7 years ago bright602 • 0
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6
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834
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ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
3.8 years ago 94133 • 0
1
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1
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1.5k
views
Error: package or namespace load failed for 'ChIPseeker' in dyn.load(file, DLLpath = DLLpath
chipseeker
3.9 years ago liucz200904 • 0
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1
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543
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How does vennplot() within Chipseeker define overlaps?
chipseeker vennplot
3.9 years ago kevin.potter12 • 0
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1
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446
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Error in getGenomicAnnoStat(peak.gr) : object 'plab' not found
ChIPseeker
updated 4.1 years ago by ★ 1.2k • written 4.1 years ago by • 0
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3
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1.1k
views
"input object should be a named list" error in ChIPseeker
ChIPseeker named list error plotAnnoBar plotDistToTSS vennplot
updated 4.2 years ago by ★ 1.2k • written 4.2 years ago by • 0
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0
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704
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problem on getpromoters on hg38
chipseeker ChIPseeker
4.2 years ago jarod_v6@libero.it ▴ 40
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3
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999
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custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
4.4 years ago andrew.gehrke • 0
50 results • Page 1 of 1
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Comment: R: problem with running time-series analysis software: Mfuzz by Kevin Blighe 3.5k
Cross-posted: https://www.biostars.org/p/9524023/
Comment: ROC plot for OPLS-DA by Eddie • 0
Hi, That was helpful. Thank you. How to do the same for the testing data?
Comment: ChIP-seq peak annotation to gene in ChIPseeker by Gyan Prakash Mishra • 0
After going through the package, I think all the peaks are annotated to genes irrespective of distance to TSS. There is also another functi…
Comment: lpsymphony compilation trouble by Cankun • 0
It's 2022 and it still works for lpsymphony_1.24.0
Comment: UniprotKB AC/ID to Entrez ID Conversion by James W. MacDonald 59k
I fixed this when Bioc 3.13 was the release version, so it should work in 3.14 and the current release. ``` > up <- UniProt.ws() > input …
Votes
A: lpsymphony compilation trouble
Answer: Robust Multi-array Average could get negative value or not?
Answer: Robust Multi-array Average could get negative value or not?
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Awards • All
Scholar to James W. MacDonald 59k
Scholar to Guido Hooiveld ★ 3.2k
Scholar to Kevin Blighe 3.5k
Scholar to SamGG ▴ 270
Prophet to johnmcma ▴ 10
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