Showing : ChIPseeker • reset
7
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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
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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
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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
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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 8.6 years ago by ▴ 50
3
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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
3
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4
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2.4k
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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 5.6 years ago by 65k • written 5.6 years ago by • 0
3
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6
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1.6k
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ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
5.8 years ago 94133 • 0
2
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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
3.4 years ago • updated 3.2 years ago Mar Mar ▴ 20
2
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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
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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
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
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 8.5 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 8.5 years ago by ★ 1.2k • written 8.5 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
882
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
2.8 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 8.5 years ago by ★ 1.2k • written 8.5 years ago by • 0
1
vote
3
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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
3.6k
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
624
views
Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
20 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
869
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
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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
5.3 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
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0
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733
views
Potential oversimplification in the overlap function
ChIPseeker
4.0 years ago konsta.kukkonen • 0
0
votes
0
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844
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
3.9 years ago hfyuan2016 • 0
0
votes
1
reply
875
views
p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 8 months ago by • 0 • written 3.7 years ago by • 0
0
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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
760
views
How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
3.5 years ago bioinfouser2 ▴ 10
0
votes
0
replies
884
views
About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
3.5 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
619
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
729
views
Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
3.4 years ago Sam ▴ 10
0
votes
0
replies
679
views
ChIPSeeker covplot function, fix yaxis
ChIPseeker
3.2 years ago jordi.planells • 0
0
votes
2
replies
997
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
698
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
50 results • Page 1 of 1
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Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Votes
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
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