Showing : ChIPseeker • reset
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how i can get the name of genes in pathway?
chipseq ChIPseeker
12 weeks ago chavaleab • 0
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152
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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
12 weeks ago 840842906 • 0
0
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1
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185
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Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 3 months ago by 63k • written 3 months ago by ▴ 50
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2
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1.2k
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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 5 months ago by 63k • written 5 months ago by • 0
1
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0
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277
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Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
9 months ago arisarkar88 ▴ 40
0
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0
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318
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
11 months ago Palmira • 0
0
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0
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847
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How to define 'distal intergenic'
ChIPseeker
12 months ago Sanghoon • 0
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1
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503
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ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
12 months ago Gyan Prakash Mishra ▴ 10
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0
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328
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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
13 months ago Swadha • 0
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0
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364
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What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
14 months ago hyjforesight • 0
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1
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1.2k
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ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
19 months ago william.ho • 0
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2
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618
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getPromoters
ChIPseeker
19 months ago guoyou88 • 0
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0
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458
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ChIPseeker, how to customize plotDistToTSS
ChIPseeker
20 months ago alexandre.blais ▴ 50
1
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3
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521
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what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
23 months ago Meghna • 0
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0
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500
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CHIPseeker- promoter gene names
ChIPseeker CHIPsee
2.0 years ago rb • 0
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1
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795
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ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 2.1 years ago by ▴ 10 • written 2.1 years ago by ▴ 10
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0
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494
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What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
2.1 years ago Sam ▴ 10
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0
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689
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Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
2.2 years ago Xiaojie Cheng • 0
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2
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704
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ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
2.2 years ago Onur Karakaslar • 0
1
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4
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1.2k
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Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
2.3 years ago Kasit • 0
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0
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394
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ChIPSeeker covplot function, fix yaxis
ChIPseeker
2.4 years ago jordi.planells • 0
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0
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487
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Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
2.5 years ago Sam ▴ 10
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2
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1.8k
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ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
2.6 years ago • updated 2.3 years ago Mar Mar ▴ 20
5
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3
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833
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importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 2.6 years ago by 63k • written 2.6 years ago by • 0
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0
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363
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Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
2.6 years ago Prasoon • 0
0
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1
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933
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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 2.6 years ago by 63k • written 2.6 years ago by • 0
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0
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601
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About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
2.6 years ago ahua217 ▴ 10
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0
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521
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How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
2.6 years ago bioinfouser2 ▴ 10
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1
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1.2k
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ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
2.8 years ago amafon95 • 0
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0
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552
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p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
2.8 years ago mwong043 • 0
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0
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562
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ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
3.0 years ago hfyuan2016 • 0
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0
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455
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Potential oversimplification in the overlap function
ChIPseeker
3.1 years ago konsta.kukkonen • 0
1
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0
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537
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Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
3.1 years ago egbastakis • 0
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1
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1.2k
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ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
3.2 years ago Assa Yeroslaviz ★ 1.5k
0
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1
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677
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ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
3.3 years ago Guandong Shang ▴ 40
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1
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1.0k
views
Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
3.7 years ago sutturka • 0
1
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2
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3.0k
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Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
3.7 years ago researcher • 0
2
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1
reply
2.4k
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Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
3.8 years ago endrebak85 ▴ 30
1
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3
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778
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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 3.9 years ago by 25k • written 3.9 years ago by ▴ 10
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1
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1.9k
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error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
4.1 years ago theodore.georgomanolis • 0
0
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1
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793
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Problem in using covplot ChIPseeker
ChIPseeker software error
4.2 years ago vasudha.sharma • 0
3
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2
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1.2k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 4.3 years ago by ★ 2.0k • written 4.3 years ago by ▴ 80
1
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1
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1.2k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 22 months ago by • 0 • written 4.4 years ago by ▴ 10
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0
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871
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How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
4.4 years ago bioinfouser2 ▴ 10
0
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2
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889
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how to get frequencies from plotDistToTSS
chipseeker
4.5 years ago KKO • 0
1
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0
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696
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ChipSeeker Flanking gene annotation
chipseeker
4.7 years ago Lauma R ▴ 10
3
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4
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1.7k
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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 4.7 years ago by 63k • written 4.7 years ago by • 0
0
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0
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598
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covplot and getChrCov function
chipseeker
4.7 years ago xiaofeiwang198266 • 0
1
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3
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1.2k
views
How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 4.7 years ago by ★ 1.2k • written 4.8 years ago by ▴ 10
0
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0
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649
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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
4.8 years ago bright602 • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k
Perhaps you are thinking of data analyses where the dependent variable is something other than expression itself. In the context of gene e…
Comment: Interpret plot from DiffBind by Chris • 0
If I want to find genes that are more open in diseased than control, I can filter out peaks that have highest log2Fold change like this, is…
Comment: Interpret plot from DiffBind by Chris • 0
Hi Rory. There are so many red dot above and below the blue line so it is hard to know which condition are more open, is that correct? Is 1…
Comment: Extract Limma Adjusted Values for Plotting by phelankj • 0
Thanks, on the normalized values using the same formula?
Answer: Extract Limma Adjusted Values for Plotting by James W. MacDonald 63k
You should use `removeBatchEffect` for that.
Votes
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
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