Showing : Chipseeker • reset
1
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9
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5.4k
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Question about ChiPseeker: plot other values in plotAvgProf2
ChiPseeker
updated 10.4 years ago by ★ 1.2k • written 10.4 years ago by ▴ 50
3
votes
10
replies
6.0k
views
ChIPseeker question: enrichPeakOverlap to find enrichment of genomic annotations in peaks from GRanges
chipseeker
updated 10.4 years ago by ★ 1.2k • written 10.4 years ago by ▴ 50
2
votes
6
replies
3.3k
views
ChIPseeker: covplot function: error with some ENCODE data sets
chiPseeker covplot ENCODE ChIpseq
10.9 years ago sarabusquets88 • 0
7
votes
11
replies
6.7k
views
annotatePeak() in ChIPseeker - how long does it take to run?
annotatePeak chipseeker chipseq org.Mm.eg.db TxDb.Mmusculus.UCSC.mm9.knownGene
updated 10.4 years ago by 25k • written 10.6 years ago by • 0
0
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3
replies
2.5k
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Chipseeker : problem running Chipseeker to ENCODE datasets
chipseeker
updated 10.8 years ago by ★ 1.2k • written 10.8 years ago by • 0
1
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11
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3.9k
views
ChIPseeker question: provide custom csAnno to plots
chipseeker
10.4 years ago francesca casalino ▴ 50
2
votes
3
replies
3.8k
views
ChIPseeker peak annotation tssRegion
chipseeker annotation chipseq
8.3 years ago lifeng.liu.biology ▴ 10
2
votes
4
replies
1.7k
views
Quantifying peaks corresponding to a purticular feature
chipseeker
10.7 years ago snigdhapola • 0
0
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2
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2.0k
views
Annotation within ChIPSeeker mismatch geneId and annotation column
ChIPseeker
10.4 years ago n.kreim ▴ 20
0
votes
2
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3.7k
views
custom annotation in annotatePeak
chipseeker Guangchuang Yu
8.2 years ago andrew.gehrke • 0
3
votes
4
replies
2.8k
views
ChIPseeker::vennplot() fails with Error in ss[[1]] : subscript out of bounds
chipseeker venn vennplot genomicranges granges
9.7 years ago enricoferrero ▴ 680
3
votes
4
replies
3.8k
views
ChIPseeker/Question about ''annoatePeak' function and for Bioconductor AnnotationData Packages for L.japonicus
chipseeker Bioconductor AnnotationData Packages Lotus japonicus ChIPseq
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
3
votes
1
reply
2.0k
views
chipseeker annotation of focused genic regions
chipseeker annotatepeak
updated 8.3 years ago by ★ 1.2k • written 8.3 years ago by • 0
5
votes
3
replies
3.1k
views
importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 10
0
votes
1
reply
3.2k
views
how to define the downstream range in ChIPseeker
ChIPseeker H3K27me3 chipseq chipseeker
updated 8.3 years ago by ★ 1.2k • written 8.3 years ago by ▴ 10
1
vote
4
replies
3.5k
views
Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
5.0 years ago Kasit • 0
5
votes
7
replies
3.2k
views
ChIPSeeker enrichPeakOverlap external dataset downloads
chipseeker chipseq chip
updated 8.2 years ago by ★ 1.2k • written 8.2 years ago by ▴ 60
0
votes
3
replies
3.0k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
8.1 years ago andrew.gehrke • 0
0
votes
3
replies
2.9k
views
"input object should be a named list" error in ChIPseeker
ChIPseeker named list error plotAnnoBar plotDistToTSS vennplot
updated 8.0 years ago by ★ 1.2k • written 8.0 years ago by • 0
0
votes
1
reply
982
views
Error in getGenomicAnnoStat(peak.gr) : object 'plab' not found
ChIPseeker
updated 7.9 years ago by ★ 1.2k • written 7.9 years ago by • 0
1
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3
replies
1.5k
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
4.7 years ago Meghna • 0
0
votes
2
replies
1.8k
views
annotatePeak error for some problem
ChIPseeker
written 2.3 years ago by • 0
0
votes
2
replies
7.1k
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 3.2 years ago by 68k • written 3.2 years ago by • 0
1
vote
3
replies
2.0k
views
ChIPseeker Error: Attempting to annotatePeaks
ChIPseeker software error
updated 10.4 years ago by ★ 1.2k • written 10.4 years ago by • 0
1
vote
4
replies
3.1k
views
ChIPseeker: Is it possible to create heatmaps / metagene plots without being centered on the TSS?
chipseq chipseeker exon start site
updated 10.4 years ago by ★ 1.2k • written 10.4 years ago by • 0
1
vote
3
replies
2.3k
views
How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 7.5 years ago by ★ 1.2k • written 7.6 years ago by ▴ 10
0
votes
1
reply
1.7k
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 3.1 years ago by 68k • written 3.1 years ago by ▴ 50
0
votes
1
reply
823
views
plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
votes
1
reply
4.5k
views
ChIPseeker: Error in annotatePeak
Sequencing GO annotate ChIPseeker Sequencing GO annotate ChIPseeker
11.8 years ago António Miguel de Jesus Domingues ▴ 510
0
votes
1
reply
1.8k
views
[ChIPseeker; feature request] More flexibility in specifying the TSS region
ChIPseeker featurerequest tss
updated 10.0 years ago by ★ 1.2k • written 10.0 years ago by ▴ 40
0
votes
1
reply
1.9k
views
ChIPseeker gene body plot
chipseeker visualization
updated 9.7 years ago by ★ 1.2k • written 9.7 years ago by ▴ 50
1
vote
2
replies
2.0k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
3.0 years ago chavaleab • 0
0
votes
8
replies
2.7k
views
significance of ChIPseq peak overlap
chipseeker
updated 9.7 years ago by ★ 1.2k • written 9.7 years ago by ▴ 10
3
votes
2
replies
2.6k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 7.0 years ago by ★ 2.1k • written 7.0 years ago by ▴ 100
0
votes
2
replies
3.7k
views
ChIPseeker annotatePeak definition
chipseeker
updated 9.5 years ago by ★ 1.2k • written 9.5 years ago by ▴ 140
1
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3
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1.8k
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 6.7 years ago by 25k • written 6.7 years ago by ▴ 20
2
votes
1
reply
5.2k
views
Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
6.5 years ago endrebak85 ▴ 40
0
votes
3
replies
1.5k
views
ChIPseeker read count calculation
chipseeker plotAvgProf
updated 9.4 years ago by ★ 1.2k • written 9.4 years ago by • 0
0
votes
1
reply
1.7k
views
How to show the fraction of peaks in CDS regions using ChIPseeker
chipseeker
updated 9.4 years ago by ★ 1.2k • written 9.4 years ago by • 0
0
votes
6
replies
3.0k
views
Chipseeker is unavabile on Linux CentOS7 ?
Bioconduct or Chipseeker CentOS7 Linux installation
updated 9.3 years ago by ★ 1.2k • written 9.3 years ago by • 0
0
votes
1
reply
1.7k
views
ChIPseeker : definition of each genomic location in annotatepeak
chipseeker
updated 9.2 years ago by ★ 1.2k • written 9.2 years ago by • 0
0
votes
1
reply
2.5k
views
ChIPseeker TSS plot
chipseeker plotAvgProf
updated 9.1 years ago by ★ 1.2k • written 9.1 years ago by • 0
0
votes
1
reply
2.1k
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 8.7 years ago by ★ 1.2k • written 8.7 years ago by • 0
2
votes
1
reply
3.8k
views
ChIPseeker mapping between keys and columns
chipseeker chipseq
updated 8.4 years ago by ▴ 690 • written 8.4 years ago by ▴ 60
0
votes
1
reply
2.4k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
0
votes
0
replies
1.4k
views
CHIPseeker- promoter gene names
ChIPseeker CHIPsee
4.8 years ago rb • 0
0
votes
0
replies
1.2k
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
3.9 years ago Swadha • 0
0
votes
0
replies
1.5k
views
Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
3.7 years ago Palmira • 0
0
votes
0
replies
1.1k
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
3.0 years ago 840842906 • 0
0
votes
0
replies
3.9k
views
How to define 'distal intergenic'
ChIPseeker
3.7 years ago Sanghoon • 0
97 results • Page 1 of 2
Recent ...
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Comment: tximeta cannot open annotation gtf? by Michael Love 43k
Yes, so this is the same type of error you would get if you tried to assemble a *SummarizedExperiment* manually with tximport + GTF process…
Answer: tximeta cannot open annotation gtf? by ATpoint ★ 5.0k
> Timeout of 60 seconds was reached You have to increase the default timeout limits for downloads, `options(timeout=3600)`. GENCODE serve…
Answer: GSEA error by James W. MacDonald 68k
At a very high level, the way non-model organisms are annotated is by using blast to find orthologs in other species that are well annotate…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Comment: Unable to find ENTREZ IDs by Adithi • 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Votes
Answer: GSEA error
Answer: OrgDb for maize
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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