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
votes
10
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4.5k
views
ChIPseeker question: enrichPeakOverlap to find enrichment of genomic annotations in peaks from GRanges
chipseeker
updated 8.5 years ago by ★ 1.2k • written 8.5 years ago by ▴ 50
2
votes
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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1.9k
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Chipseeker : problem running Chipseeker to ENCODE datasets
chipseeker
updated 8.9 years ago by ★ 1.2k • written 8.9 years ago by • 0
7
votes
11
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4.8k
views
annotatePeak() in ChIPseeker - how long does it take to run?
annotatePeak chipseeker chipseq org.Mm.eg.db TxDb.Mmusculus.UCSC.mm9.knownGene
updated 8.5 years ago by 25k • written 8.7 years ago by • 0
2
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4
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1.2k
views
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
views
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
6.4 years ago lifeng.liu.biology ▴ 10
0
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2
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1.4k
views
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
reply
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
1.2k
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
replies
1.3k
views
importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 3.4 years ago by 65k • written 3.4 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
replies
1.9k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
6.3 years ago andrew.gehrke • 0
0
votes
3
replies
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
872
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
354
views
annotatePeak error for some problem
ChIPseeker
updated 5 months ago by 65k • written 5 months ago by • 0
0
votes
2
replies
3.1k
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 16 months ago by 65k • written 16 months ago by • 0
0
votes
1
reply
675
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
vote
3
replies
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
792
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
294
views
plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 5 months ago by 65k • written 5 months ago by • 0
0
votes
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
votes
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
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8
replies
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
979
views
ChIPseeker read count calculation
chipseeker plotAvgProf
updated 7.5 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
replies
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 6.8 years ago by ★ 1.2k • written 6.9 years ago by • 0
0
votes
0
replies
678
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
767
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
556
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
votes
0
replies
1.9k
views
How to define 'distal intergenic'
ChIPseeker
22 months ago Sanghoon • 0
0
votes
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: Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia) by christianhilton64 • 0
I'm less familiar with the specifics of GSVA, but I'm curious about the overall goal of this analysis. Could you provide a high-level summa…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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