Showing : Chipseeker • reset
1
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Question about ChiPseeker: plot other values in plotAvgProf2
ChiPseeker
updated 8.5 years ago by ★ 1.2k • written 8.5 years ago by ▴ 50
3
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10
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4.5k
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ChIPseeker question: enrichPeakOverlap to find enrichment of genomic annotations in peaks from GRanges
chipseeker
updated 8.5 years ago by ★ 1.2k • written 8.6 years ago by ▴ 50
2
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6
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2.5k
views
ChIPseeker: covplot function: error with some ENCODE data sets
chiPseeker covplot ENCODE ChIpseq
9.0 years ago sarabusquets88 • 0
0
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3
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2.0k
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Chipseeker : problem running Chipseeker to ENCODE datasets
chipseeker
updated 8.9 years ago by ★ 1.2k • written 9.0 years ago by • 0
7
votes
11
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4.8k
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annotatePeak() in ChIPseeker - how long does it take to run?
annotatePeak chipseeker chipseq org.Mm.eg.db TxDb.Mmusculus.UCSC.mm9.knownGene
updated 8.6 years ago by 25k • written 8.8 years ago by • 0
2
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4
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1.2k
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Quantifying peaks corresponding to a purticular feature
chipseeker
8.9 years ago snigdhapola • 0
0
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2
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2.6k
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custom annotation in annotatePeak
chipseeker Guangchuang Yu
6.3 years ago andrew.gehrke • 0
3
votes
4
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2.0k
views
ChIPseeker::vennplot() fails with Error in ss[[1]] : subscript out of bounds
chipseeker venn vennplot genomicranges granges
7.8 years ago enricoferrero ▴ 660
2
votes
3
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2.6k
views
ChIPseeker peak annotation tssRegion
chipseeker annotation chipseq
6.5 years ago • updated 6.4 years ago lifeng.liu.biology ▴ 10
0
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2
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1.4k
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Annotation within ChIPSeeker mismatch geneId and annotation column
ChIPseeker
8.5 years ago n.kreim ▴ 20
3
votes
4
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2.4k
views
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
1
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11
replies
2.8k
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ChIPseeker question: provide custom csAnno to plots
chipseeker
8.5 years ago francesca casalino ▴ 50
2
votes
1
reply
2.5k
views
ChIPseeker mapping between keys and columns
chipseeker chipseq
updated 6.6 years ago by ▴ 680 • written 6.6 years ago by ▴ 60
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
3
votes
1
reply
1.3k
views
chipseeker annotation of focused genic regions
chipseeker annotatepeak
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by • 0
5
votes
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 3.5 years ago by ▴ 10
0
votes
1
reply
2.2k
views
how to define the downstream range in ChIPseeker
ChIPseeker H3K27me3 chipseq chipseeker
updated 6.4 years ago by ★ 1.2k • written 6.4 years ago by ▴ 10
1
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4
replies
2.0k
views
Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
3.2 years ago Kasit • 0
5
votes
7
replies
2.2k
views
ChIPSeeker enrichPeakOverlap external dataset downloads
chipseeker chipseq chip
updated 6.3 years ago by ★ 1.2k • written 6.3 years ago by ▴ 60
0
votes
3
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1.9k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
6.3 years ago andrew.gehrke • 0
0
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3
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2.0k
views
"input object should be a named list" error in ChIPseeker
ChIPseeker named list error plotAnnoBar plotDistToTSS vennplot
updated 6.1 years ago by ★ 1.2k • written 6.1 years ago by • 0
1
vote
3
replies
880
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
2.8 years ago Meghna • 0
0
votes
1
reply
359
views
annotatePeak error for some problem
ChIPseeker
updated 5 months ago by 65k • written 5 months ago by • 0
0
votes
2
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3.2k
views
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 16 months ago by 65k • written 16 months ago by • 0
0
votes
1
reply
678
views
Error in getGenomicAnnoStat(peak.gr) : object 'plab' not found
ChIPseeker
updated 6.0 years ago by ★ 1.2k • written 6.0 years ago by • 0
1
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3
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1.4k
views
ChIPseeker Error: Attempting to annotatePeaks
ChIPseeker software error
updated 8.5 years ago by ★ 1.2k • written 8.5 years ago by • 0
1
vote
4
replies
2.1k
views
ChIPseeker: Is it possible to create heatmaps / metagene plots without being centered on the TSS?
chipseq chipseeker exon start site
updated 8.5 years ago by ★ 1.2k • written 8.5 years ago by • 0
1
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3
replies
1.5k
views
How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 5.6 years ago by ★ 1.2k • written 5.7 years ago by ▴ 10
0
votes
1
reply
802
views
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
0
votes
1
reply
301
views
plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 5 months ago by 65k • written 5 months ago by • 0
0
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1
reply
3.1k
views
ChIPseeker: Error in annotatePeak
Sequencing GO annotate ChIPseeker Sequencing GO annotate ChIPseeker
10.0 years ago António Miguel de Jesus Domingues ▴ 490
0
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1
reply
1.3k
views
[ChIPseeker; feature request] More flexibility in specifying the TSS region
ChIPseeker featurerequest tss
updated 8.2 years ago by ★ 1.2k • written 8.2 years ago by ▴ 40
1
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2
replies
1.0k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
13 months ago chavaleab • 0
0
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1
reply
1.4k
views
ChIPseeker gene body plot
chipseeker visualization
updated 7.9 years ago by ★ 1.2k • written 7.9 years ago by ▴ 40
3
votes
2
replies
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
0
votes
8
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2.0k
views
significance of ChIPseq peak overlap
chipseeker
updated 7.8 years ago by ★ 1.2k • written 7.8 years ago by ▴ 10
0
votes
2
replies
2.4k
views
ChIPseeker annotatePeak definition
chipseeker
updated 7.6 years ago by ★ 1.2k • written 7.6 years ago by ▴ 140
1
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3
replies
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
2
votes
1
reply
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
0
votes
3
replies
985
views
ChIPseeker read count calculation
chipseeker plotAvgProf
updated 7.6 years ago by ★ 1.2k • written 7.6 years ago by • 0
0
votes
1
reply
1.3k
views
How to show the fraction of peaks in CDS regions using ChIPseeker
chipseeker
updated 7.5 years ago by ★ 1.2k • written 7.5 years ago by • 0
0
votes
6
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2.3k
views
Chipseeker is unavabile on Linux CentOS7 ?
Bioconduct or Chipseeker CentOS7 Linux installation
updated 7.5 years ago by ★ 1.2k • written 7.5 years ago by • 0
0
votes
1
reply
1.3k
views
ChIPseeker : definition of each genomic location in annotatepeak
chipseeker
updated 7.3 years ago by ★ 1.2k • written 7.3 years ago by • 0
0
votes
1
reply
1.8k
views
ChIPseeker TSS plot
chipseeker plotAvgProf
updated 7.2 years ago by ★ 1.2k • written 7.2 years ago by • 0
0
votes
1
reply
1.4k
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 6.9 years ago by ★ 1.2k • written 6.9 years ago by • 0
0
votes
0
replies
683
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
24 months ago Swadha • 0
0
votes
0
replies
772
views
Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
22 months ago Palmira • 0
0
votes
0
replies
561
views
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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0
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1.9k
views
How to define 'distal intergenic'
ChIPseeker
22 months ago Sanghoon • 0
0
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0
replies
1.0k
views
problem on getpromoters on hg38
chipseeker ChIPseeker
6.2 years ago jarod_v6@libero.it ▴ 40
50 results • Page 1 of 1
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Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Answer: get BM error by James W. MacDonald 65k
The genes you present are orthologous mappings from D. rerio to other teleost fishes, so it is probably going to be difficult to map to NCB…
Answer: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
You can also use a combination of the `org.Hs.eg.db` and `GO.db` packages. ``` > library(GO.db) > library(org.Hs.eg.db) > go <- m…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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