Showing : chiPseeker • reset
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[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
17 hours ago Henry ▴ 10
0
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1
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294
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plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 4 months ago by 65k • written 4 months ago by • 0
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1
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346
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annotatePeak error for some problem
ChIPseeker
updated 5 months ago by 65k • written 5 months ago by • 0
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1
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867
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p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 8 months ago by • 0 • written 3.7 years ago by • 0
1
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2
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1.0k
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how i can get the name of genes in pathway?
chipseq ChIPseeker
13 months ago chavaleab • 0
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0
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553
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Can ChiPseeker be as highly customizable as "computeMatrix"? for example if I want to plot the distribution of genes on the TAD boundary?
deeptools ChIPseeker
13 months ago 840842906 • 0
0
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1
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784
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Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 14 months ago by 65k • written 14 months ago by ▴ 50
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2
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3.1k
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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 15 months ago by 65k • written 15 months ago by • 0
1
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613
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Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
20 months ago arisarkar88 ▴ 40
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0
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762
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
21 months ago Palmira • 0
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1.8k
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How to define 'distal intergenic'
ChIPseeker
22 months ago Sanghoon • 0
0
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1
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945
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ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
23 months ago Gyan Prakash Mishra ▴ 10
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0
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674
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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 months ago Swadha • 0
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0
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689
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What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
2.1 years ago hyjforesight • 0
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1
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1.6k
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ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
2.4 years ago william.ho • 0
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2
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950
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getPromoters
ChIPseeker
2.5 years ago guoyou88 • 0
0
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0
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717
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ChIPseeker, how to customize plotDistToTSS
ChIPseeker
2.5 years ago alexandre.blais ▴ 50
1
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1
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1.7k
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ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 2.7 years ago by • 0 • written 5.3 years ago by ▴ 10
1
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3
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864
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what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
2.8 years ago Meghna • 0
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0
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789
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CHIPseeker- promoter gene names
ChIPseeker CHIPsee
2.9 years ago rb • 0
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1
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1.3k
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ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 3.0 years ago by ▴ 10 • written 3.0 years ago by ▴ 10
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0
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804
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What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
3.0 years ago Sam ▴ 10
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0
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1.0k
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Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
3.0 years ago Xiaojie Cheng • 0
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2
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986
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ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
3.1 years ago Onur Karakaslar • 0
1
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4
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1.9k
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Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
3.1 years ago Kasit • 0
2
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2
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2.4k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
3.4 years ago • updated 3.2 years ago Mar Mar ▴ 20
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0
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669
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ChIPSeeker covplot function, fix yaxis
ChIPseeker
3.2 years ago jordi.planells • 0
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0
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721
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Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
3.4 years ago Sam ▴ 10
5
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3
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1.3k
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importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 3.4 years ago by 65k • written 3.4 years ago by ▴ 10
0
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0
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611
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Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
3.4 years ago Prasoon • 0
0
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1
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1.4k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 3.5 years ago by 65k • written 3.5 years ago by • 0
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0
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876
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About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
3.5 years ago ahua217 ▴ 10
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0
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752
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How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
3.5 years ago bioinfouser2 ▴ 10
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1
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1.8k
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ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
3.6 years ago amafon95 • 0
0
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0
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836
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
3.9 years ago hfyuan2016 • 0
0
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0
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726
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Potential oversimplification in the overlap function
ChIPseeker
3.9 years ago konsta.kukkonen • 0
1
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0
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856
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Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
3.9 years ago egbastakis • 0
0
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1
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1.6k
views
ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
4.0 years ago Assa Yeroslaviz ★ 1.5k
0
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1
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1.0k
views
ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
4.2 years ago Guandong Shang ▴ 40
0
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1
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1.6k
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Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
4.6 years ago sutturka • 0
1
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2
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3.6k
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Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
4.6 years ago researcher • 0
2
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1
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3.5k
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
1
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3
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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
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1
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2.6k
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error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
4.9 years ago Theo ▴ 10
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1
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1.1k
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Problem in using covplot ChIPseeker
ChIPseeker software error
5.1 years ago vasudha.sharma • 0
3
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2
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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
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0
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1.1k
views
How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
5.3 years ago bioinfouser2 ▴ 10
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2
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1.2k
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how to get frequencies from plotDistToTSS
chipseeker
5.3 years ago KKO • 0
1
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0
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1.0k
views
ChipSeeker Flanking gene annotation
chipseeker
5.5 years ago Lauma R ▴ 10
3
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4
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2.4k
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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 5.6 years ago by 65k • written 5.6 years ago by • 0
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Answer: Differentially expressed genes in monocle pseudotime by Gordon Smyth 50k
You might try the methods in this paper: Cheng J, Smyth GK*, Chen Y* (2023). Unraveling the timeline of gene expression: A pseudotempora…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you Michael for your attention to my question. I am truly grateful. I subsetted the data using lines of codes to include only the g…
Comment: [DiffBind] Obtaining normalization factors by Henry ▴ 10
I see, thank you for your suggestion! I managed to use a separate RLE normalization to obtain the size factors.
Answer: Memory errors using read.bismark? by Peter Hickey ▴ 690
Thanks for sharing an example file. This is a very large non-CpG methylation dataset, which are tricky to work with for a number of reason…
Comment: Reading huge bismark coverage files using bbseq::read.bismark by Peter Hickey ▴ 690
Superficially, your issue is similar to [https://github.com/hansenlab/bsseq/issues/136](https://github.com/hansenlab/bsseq/issues/136). You…
Votes
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
Comment: DESeq2 - Plot Nr. Genes vs Variance explained in PCA
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