Showing : ChIPseeker • reset
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ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
8 days ago Anton01 • 0
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87
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[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
5 weeks ago Henry ▴ 10
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1
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331
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plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 6 months ago by 66k • written 6 months ago by • 0
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1
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433
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annotatePeak error for some problem
ChIPseeker
updated 6 months ago by 66k • written 6 months ago by • 0
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1
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911
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p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 9 months ago by • 0 • written 3.8 years ago by • 0
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2
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1.1k
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how i can get the name of genes in pathway?
chipseq ChIPseeker
14 months ago chavaleab • 0
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581
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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
14 months ago 840842906 • 0
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1
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851
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Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 15 months ago by 66k • written 15 months ago by ▴ 50
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2
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3.4k
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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 17 months ago by 66k • written 17 months ago by • 0
1
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660
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Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
21 months ago arisarkar88 ▴ 40
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0
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812
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
23 months ago Palmira • 0
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0
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2.0k
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How to define 'distal intergenic'
ChIPseeker
23 months ago Sanghoon • 0
0
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1
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995
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ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
2.0 years ago Gyan Prakash Mishra ▴ 10
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0
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705
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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
2.1 years ago Swadha • 0
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0
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724
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What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
2.2 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
2.6 years ago william.ho • 0
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2
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1.0k
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getPromoters
ChIPseeker
2.6 years ago guoyou88 • 0
0
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0
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750
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ChIPseeker, how to customize plotDistToTSS
ChIPseeker
2.6 years ago alexandre.blais ▴ 50
1
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1
reply
1.7k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 2.8 years ago by • 0 • written 5.4 years ago by ▴ 10
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3
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910
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what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
2.9 years ago Meghna • 0
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0
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830
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CHIPseeker- promoter gene names
ChIPseeker CHIPsee
3.0 years ago rb • 0
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1
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1.4k
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ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 3.1 years ago by ▴ 10 • written 3.1 years ago by ▴ 10
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0
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851
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What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
3.1 years ago Sam ▴ 10
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0
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1.1k
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Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
3.1 years ago Xiaojie Cheng • 0
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2
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1.0k
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ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
3.2 years ago Onur Karakaslar • 0
1
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4
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2.1k
views
Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
3.2 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
3.5 years ago • updated 3.3 years ago Mar Mar ▴ 20
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704
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ChIPSeeker covplot function, fix yaxis
ChIPseeker
3.3 years ago jordi.planells • 0
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756
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Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
3.5 years ago Sam ▴ 10
5
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3
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1.4k
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importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 3.5 years ago by 66k • written 3.5 years ago by ▴ 10
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0
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644
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Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
3.5 years ago Prasoon • 0
0
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1
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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 66k • written 3.6 years ago by • 0
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0
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914
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About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
3.6 years ago ahua217 ▴ 10
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0
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778
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How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
3.6 years ago bioinfouser2 ▴ 10
0
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1
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1.8k
views
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
3.7 years ago amafon95 • 0
0
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0
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875
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
4.0 years ago hfyuan2016 • 0
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0
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757
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Potential oversimplification in the overlap function
ChIPseeker
4.0 years ago konsta.kukkonen • 0
1
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0
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896
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Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
4.0 years ago egbastakis • 0
0
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1
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1.7k
views
ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
4.1 years ago Assa Yeroslaviz ★ 1.5k
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1
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1.0k
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ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
4.3 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
4.7 years ago sutturka • 0
1
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2
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3.7k
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Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
4.7 years ago researcher • 0
2
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1
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3.7k
views
Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
4.8 years ago endrebak85 ▴ 40
1
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3
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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
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1
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2.6k
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error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
5.0 years ago Theo ▴ 10
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1
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1.1k
views
Problem in using covplot ChIPseeker
ChIPseeker software error
5.2 years ago vasudha.sharma • 0
3
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2
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1.8k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 5.3 years ago by ★ 2.0k • written 5.3 years ago by ▴ 100
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0
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1.2k
views
How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
5.4 years ago bioinfouser2 ▴ 10
0
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2
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1.2k
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how to get frequencies from plotDistToTSS
chipseeker
5.4 years ago KKO • 0
1
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0
replies
1.0k
views
ChipSeeker Flanking gene annotation
chipseeker
5.6 years ago Lauma R ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by Wei Shi ★ 3.6k
Your bam file names should be stored in a vector and then provided to the `files` parameter.
Comment: Volcano plot of scRNA-seq data not "centered" by Michael Love 42k
Agree with @atpoint Depending on the "groups" in single cell, the question of DE can be not well defined without inserting additional inf…
Answer: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
Sounds like a normalization problem, but I am not sure how to help with that. Indeed you can use control genes, for example use the top 20%…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by ATpoint ★ 4.2k
I was talking about the command line version.
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
I tried reading in the .csv version of the SAF with header = F and I'm still getting an error. I'm running: ``` counts <- featureCounts( …
Votes
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Seurat to SingleCellExperiment Converting error in MAC
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