Showing : ChIPseeker • reset
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ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 3 days ago by ▴ 10 • written 5 days ago by • 0
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30
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What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
7 days ago Sam ▴ 10
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53
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Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
18 days ago Xiaojie Cheng • 0
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2
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166
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ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
4 weeks ago • updated 27 days ago Onur Karakaslar • 0
1
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4
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127
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Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
8 weeks ago • updated 7 weeks ago Kasit • 0
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51
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ChIPSeeker covplot function, fix yaxis
ChIPseeker
12 weeks ago jordi.planells • 0
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80
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Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
4 months ago Sam ▴ 10
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2
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291
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ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
5 months ago • updated 10 weeks ago Mar Mar • 0
5
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3
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136
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importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 5 months ago by 56k • written 5 months ago by • 0
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55
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Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
5 months ago Prasoon • 0
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1
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79
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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 5 months ago by 56k • written 5 months ago by • 0
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116
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About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
6 months ago ahua217 ▴ 10
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0
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121
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How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
6 months ago bioinfouser2 ▴ 10
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1
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167
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ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
7 months ago amafon95 • 0
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143
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p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
8 months ago mwong043 • 0
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147
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ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
11 months ago hfyuan2016 • 0
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126
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Potential oversimplification in the overlap function
ChIPseeker
11 months ago konsta.kukkonen • 0
1
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0
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131
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Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
11 months ago egbastakis • 0
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1
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145
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ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
12 months ago Assa Yeroslaviz ★ 1.5k
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1
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165
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ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
14 months ago shangguandong1996 ▴ 20
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1
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277
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Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
19 months ago sutturka • 0
1
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2
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1.3k
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Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
19 months ago researcher • 0
2
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1
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310
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Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
20 months ago endrebak85 ▴ 30
1
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3
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296
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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 21 months ago by 25k • written 21 months ago by ▴ 10
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1
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644
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error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
23 months ago theodore.georgomanolis • 0
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1
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363
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Problem in using covplot ChIPseeker
ChIPseeker software error
2.1 years ago vasudha.sharma • 0
3
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2
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504
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How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 2.2 years ago by ★ 1.9k • written 2.2 years ago by ▴ 60
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459
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ChIPseeker genomicAnnotationPriority
annotation chipseeker
2.3 years ago dolata • 0
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385
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How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
2.3 years ago bioinfouser2 ▴ 10
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2
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455
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how to get frequencies from plotDistToTSS
chipseeker
2.4 years ago KKO • 0
1
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372
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ChipSeeker Flanking gene annotation
chipseeker
2.6 years ago Lauma R ▴ 10
3
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4
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647
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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
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312
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covplot and getChrCov function
chipseeker
2.6 years ago xiaofeiwang198266 • 0
1
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3
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616
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How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 2.6 years ago by ★ 1.2k • written 2.7 years ago by ▴ 10
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318
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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
2.7 years ago bright602 • 0
3
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6
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536
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ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
2.7 years ago 94133 • 0
1
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1
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1.1k
views
Error: package or namespace load failed for 'ChIPseeker' in dyn.load(file, DLLpath = DLLpath
chipseeker
2.8 years ago liucz200904 • 0
0
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1
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351
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How does vennplot() within Chipseeker define overlaps?
chipseeker vennplot
2.8 years ago kevin.potter12 • 0
0
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1
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310
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Error in getGenomicAnnoStat(peak.gr) : object 'plab' not found
ChIPseeker
updated 3.0 years ago by ★ 1.2k • written 3.0 years ago by • 0
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3
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767
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"input object should be a named list" error in ChIPseeker
ChIPseeker named list error plotAnnoBar plotDistToTSS vennplot
updated 3.1 years ago by ★ 1.2k • written 3.1 years ago by • 0
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531
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problem on getpromoters on hg38
chipseeker ChIPseeker
3.2 years ago jarod_v6@libero.it ▴ 40
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3
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706
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custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
3.3 years ago andrew.gehrke • 0
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2
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976
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custom annotation in annotatePeak
chipseeker Guangchuang Yu
3.3 years ago andrew.gehrke • 0
5
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7
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808
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ChIPSeeker enrichPeakOverlap external dataset downloads
chipseeker chipseq chip
updated 3.3 years ago by ★ 1.2k • written 3.3 years ago by ▴ 60
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0
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775
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Intergenic assigned to genes by ChIPseeker
chipseeker txdb.mmusculus.ucsc.mm10.knowngene
3.3 years ago doan.dinh • 0
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1
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790
views
how to define the downstream range in ChIPseeker
ChIPseeker H3K27me3 chipseq chipseeker
updated 3.4 years ago by ★ 1.2k • written 3.4 years ago by ▴ 10
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0
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494
views
Removing/combining specific annotation categories in ChIPSeeker plots/analysis
chipseeker chipseq annotation
3.4 years ago rbronste ▴ 60
2
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3
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1000
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ChIPseeker peak annotation tssRegion
chipseeker annotation chipseq
3.4 years ago lifeng.liu.biology ▴ 10
2
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1
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480
views
chipseeker annotation of focused genic regions
chipseeker annotatepeak
updated 3.5 years ago by ★ 1.2k • written 3.5 years ago by • 0
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0
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537
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Assigning stats to differential peak locations relative to TSS
chipseeker chipseq statistics
3.6 years ago rbronste ▴ 60
77 results • Page 1 of 2
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Answer: unable to forge custom BSgenome after update by Hervé Pagès 14k
Hi, You need to specify the `circ_seqs` field in your seed file. `forgeBSgenomeDataPkg()` needs to know which sequences are circular …
Comment: How to apply limma-trend or voom to batch corrected single cell data? (non-integ by hainct • 0
Thank you @alun
Comment: EnhancedVolcano plot with colCustom by Neeraja Vegesna ▴ 10
Hi Kevin, It worked once I added `names(keyvals.colour1)[keyvals.colour1 == '#8F8F8F'] <- 'NA'`. ![volcanoplot][1] Thanks a lot for you…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza by mwong043 • 0
Thanks Rory. I tried the first method by defining a vector containing the normalisation factors for my samples and it worked. I am just wo…
Comment: EnhancedVolcano plot with colCustom by Kevin Blighe 2.8k
Hi, that's great that it works with a lower number of groups. Can you re-check the logic flow when you are using more groups? *EnhancedVolc…
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mgcv not updating
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Comment: EnhancedVolcano plot with colCustom
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