Showing : ChiPseeker • reset
7
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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
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
5
votes
3
replies
1.3k
views
importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 3.5 years ago by 65k • written 3.5 years ago by ▴ 10
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
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
3
votes
10
replies
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 8.6 years ago by ▴ 50
3
votes
4
replies
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
3
votes
4
replies
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
3
votes
6
replies
1.6k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
5.8 years ago 94133 • 0
2
votes
4
replies
1.2k
views
Quantifying peaks corresponding to a purticular feature
chipseeker
8.9 years ago snigdhapola • 0
2
votes
2
replies
2.4k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
3.5 years ago • updated 3.2 years ago Mar Mar ▴ 20
2
votes
6
replies
2.5k
views
ChIPseeker: covplot function: error with some ENCODE data sets
chiPseeker covplot ENCODE ChIpseq
9.0 years ago sarabusquets88 • 0
2
votes
3
replies
2.6k
views
ChIPseeker peak annotation tssRegion
chipseeker annotation chipseq
6.5 years ago lifeng.liu.biology ▴ 10
2
votes
1
reply
3.6k
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
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
1
vote
9
replies
3.8k
views
Question about ChiPseeker: plot other values in plotAvgProf2
ChiPseeker
updated 8.5 years ago by ★ 1.2k • written 8.6 years ago by ▴ 50
1
vote
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
1
vote
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
1
vote
3
replies
1.4k
views
ChIPseeker Error: Attempting to annotatePeaks
ChIPseeker software error
updated 8.6 years ago by ★ 1.2k • written 8.6 years ago by • 0
1
vote
0
replies
1.0k
views
ChipSeeker Flanking gene annotation
chipseeker
5.6 years ago Lauma R ▴ 10
1
vote
1
reply
1.7k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 2.8 years ago by • 0 • written 5.3 years ago by ▴ 10
1
vote
3
replies
890
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
2.9 years ago Meghna • 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 8.6 years ago by ★ 1.2k • written 8.6 years ago by • 0
1
vote
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
1
vote
2
replies
3.7k
views
Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
4.6 years ago researcher • 0
1
vote
0
replies
641
views
Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
21 months ago arisarkar88 ▴ 40
1
vote
11
replies
2.8k
views
ChIPseeker question: provide custom csAnno to plots
chipseeker
8.5 years ago francesca casalino ▴ 50
1
vote
0
replies
878
views
Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
4.0 years ago egbastakis • 0
1
vote
2
replies
1.0k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
13 months ago chavaleab • 0
1
vote
1
reply
2.1k
views
Error: package or namespace load failed for 'ChIPseeker' in dyn.load(file, DLLpath = DLLpath
chipseeker
5.8 years ago liucz200904 • 0
0
votes
2
replies
1.2k
views
how to get frequencies from plotDistToTSS
chipseeker
5.4 years ago KKO • 0
0
votes
0
replies
1.1k
views
How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
5.4 years ago bioinfouser2 ▴ 10
0
votes
1
reply
1.1k
views
Problem in using covplot ChIPseeker
ChIPseeker software error
5.1 years ago vasudha.sharma • 0
0
votes
1
reply
2.6k
views
error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
5.0 years ago Theo ▴ 10
0
votes
1
reply
1.6k
views
Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
4.6 years ago sutturka • 0
0
votes
1
reply
1.0k
views
ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
4.2 years ago Guandong Shang ▴ 40
0
votes
0
replies
741
views
Potential oversimplification in the overlap function
ChIPseeker
4.0 years ago konsta.kukkonen • 0
0
votes
0
replies
860
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
4.0 years ago hfyuan2016 • 0
0
votes
1
reply
888
views
p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 9 months ago by • 0 • written 3.8 years ago by • 0
0
votes
1
reply
1.8k
views
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
3.7 years ago amafon95 • 0
0
votes
0
replies
766
views
How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
3.6 years ago bioinfouser2 ▴ 10
0
votes
0
replies
892
views
About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
3.6 years ago ahua217 ▴ 10
0
votes
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
0
votes
0
replies
630
views
Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
3.5 years ago Prasoon • 0
0
votes
0
replies
739
views
Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
3.4 years ago Sam ▴ 10
0
votes
0
replies
686
views
ChIPSeeker covplot function, fix yaxis
ChIPseeker
3.3 years ago jordi.planells • 0
0
votes
2
replies
1.0k
views
ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
3.1 years ago Onur Karakaslar • 0
0
votes
0
replies
1.0k
views
Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
3.1 years ago Xiaojie Cheng • 0
0
votes
0
replies
709
views
What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
2.1 years ago hyjforesight • 0
0
votes
1
reply
1.6k
views
ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
2.5 years ago william.ho • 0
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Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Comment: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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