Showing : ChIPseeker • reset
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ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
10 weeks ago Anton01 • 0
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131
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[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
3 months ago Henry ▴ 10
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1
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393
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plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 8 months ago by 66k • written 8 months ago by • 0
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2
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570
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annotatePeak error for some problem
ChIPseeker
written 8 months ago by • 0
1
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2
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1.2k
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how i can get the name of genes in pathway?
chipseq ChIPseeker
16 months ago chavaleab • 0
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628
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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
16 months ago 840842906 • 0
0
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1
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966
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Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 17 months ago by 66k • written 17 months ago by ▴ 50
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2
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3.8k
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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 19 months ago by 66k • written 19 months ago by • 0
1
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721
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Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
23 months ago arisarkar88 ▴ 40
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0
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888
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
2.1 years ago Palmira • 0
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2.2k
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How to define 'distal intergenic'
ChIPseeker
2.1 years ago Sanghoon • 0
0
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1
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1.1k
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ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
2.2 years ago Gyan Prakash Mishra ▴ 10
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0
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761
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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
2.2 years ago Swadha • 0
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0
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790
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What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
2.3 years ago hyjforesight • 0
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1
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1.7k
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ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
2.7 years ago william.ho • 0
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2
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1.1k
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getPromoters
ChIPseeker
2.8 years ago guoyou88 • 0
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0
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804
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ChIPseeker, how to customize plotDistToTSS
ChIPseeker
2.8 years ago alexandre.blais ▴ 50
1
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3
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970
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
3.1 years ago Meghna • 0
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0
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886
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CHIPseeker- promoter gene names
ChIPseeker CHIPsee
3.2 years ago rb • 0
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1
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1.5k
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ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 3.3 years ago by ▴ 10 • written 3.3 years ago by ▴ 10
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0
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901
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What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
3.3 years ago Sam ▴ 10
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1.1k
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Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
3.3 years ago Xiaojie Cheng • 0
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2
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1.1k
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ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
3.4 years ago • updated 3.3 years ago Onur Karakaslar • 0
1
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4
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2.3k
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Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
3.4 years ago Kasit • 0
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0
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749
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ChIPSeeker covplot function, fix yaxis
ChIPseeker
3.5 years ago jordi.planells • 0
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0
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799
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Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
3.7 years ago • updated 3.6 years ago Sam ▴ 10
2
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2
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2.5k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
3.7 years ago • updated 3.5 years ago Mar Mar ▴ 20
5
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3
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1.6k
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importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 3.7 years ago by 66k • written 3.7 years ago by ▴ 10
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0
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682
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Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
3.7 years ago Prasoon • 0
0
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1
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1.6k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 3.7 years ago by 66k • written 3.7 years ago by • 0
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0
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970
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About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
3.8 years ago ahua217 ▴ 10
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0
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821
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How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
3.8 years ago bioinfouser2 ▴ 10
2
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1
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2.0k
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ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
3.9 years ago amafon95 ▴ 20
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1
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965
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p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 11 months ago by • 0 • written 4.0 years ago by • 0
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0
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938
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ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
4.2 years ago hfyuan2016 • 0
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0
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797
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Potential oversimplification in the overlap function
ChIPseeker
4.2 years ago konsta.kukkonen • 0
1
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0
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938
views
Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
4.2 years ago egbastakis • 0
0
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1
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1.8k
views
ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
4.3 years ago Assa Yeroslaviz ★ 1.5k
0
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1
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1.1k
views
ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
4.4 years ago Guandong Shang ▴ 40
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1
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1.7k
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Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
4.8 years ago sutturka • 0
1
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2
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3.8k
views
Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
4.9 years ago researcher • 0
2
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1
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3.9k
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Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
4.9 years ago endrebak85 ▴ 40
1
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3
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1.2k
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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 5.1 years ago by 25k • written 5.1 years ago by ▴ 10
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1
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2.8k
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error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
5.2 years ago Theo ▴ 10
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1
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1.2k
views
Problem in using covplot ChIPseeker
ChIPseeker software error
5.4 years ago vasudha.sharma • 0
3
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2
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1.9k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 5.4 years ago by ★ 2.1k • written 5.4 years ago by ▴ 100
1
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1
reply
1.8k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 3.0 years ago by • 0 • written 5.6 years ago by ▴ 10
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0
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1.2k
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How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
5.6 years ago bioinfouser2 ▴ 10
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2
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1.3k
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how to get frequencies from plotDistToTSS
chipseeker
5.6 years ago KKO • 0
1
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0
replies
1.1k
views
ChipSeeker Flanking gene annotation
chipseeker
5.8 years ago Lauma R ▴ 10
50 results • Page 1 of 1
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
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Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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