Showing : ChIPseeker • reset
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ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
12 months ago Anton01 • 0
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0
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356
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[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
13 months ago Henry ▴ 10
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1
reply
630
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plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 18 months ago by 68k • written 18 months ago by • 0
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2
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1.3k
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annotatePeak error for some problem
ChIPseeker
written 18 months ago by • 0
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2
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1.6k
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how i can get the name of genes in pathway?
chipseq ChIPseeker
2.2 years ago chavaleab • 0
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0
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915
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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
2.2 years ago 840842906 • 0
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1
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1.4k
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Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 50
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2
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6.1k
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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 2.4 years ago by 68k • written 2.4 years ago by • 0
1
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985
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Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
2.8 years ago arisarkar88 ▴ 40
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1.2k
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
2.9 years ago Palmira • 0
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3.3k
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How to define 'distal intergenic'
ChIPseeker
3.0 years ago Sanghoon • 0
0
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1
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1.5k
views
ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
3.0 years ago Gyan Prakash Mishra ▴ 10
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0
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974
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Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
3.1 years ago Swadha • 0
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1.0k
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What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
3.1 years ago hyjforesight • 0
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1
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2.2k
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ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
3.5 years ago william.ho • 0
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2
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1.4k
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getPromoters
ChIPseeker
3.6 years ago guoyou88 • 0
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0
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1.0k
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ChIPseeker, how to customize plotDistToTSS
ChIPseeker
3.6 years ago alexandre.blais ▴ 50
1
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3
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1.2k
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
3.9 years ago Meghna • 0
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0
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1.2k
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CHIPseeker- promoter gene names
ChIPseeker CHIPsee
4.0 years ago rb • 0
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1
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2.0k
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ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 4.1 years ago by ▴ 10 • written 4.1 years ago by ▴ 10
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0
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1.1k
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What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
4.1 years ago Sam ▴ 10
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0
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1.4k
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Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
4.1 years ago Xiaojie Cheng • 0
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2
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1.3k
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ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
4.2 years ago Onur Karakaslar • 0
1
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4
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2.9k
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Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
4.2 years ago Kasit • 0
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0
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982
views
ChIPSeeker covplot function, fix yaxis
ChIPseeker
4.3 years ago jordi.planells • 0
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0
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979
views
Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
4.5 years ago Sam ▴ 10
2
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2
replies
2.9k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
4.5 years ago • updated 4.3 years ago Mar Mar ▴ 20
5
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3
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2.6k
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importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 10
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0
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826
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Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
4.5 years ago Prasoon • 0
0
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1
reply
2.1k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
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0
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1.2k
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About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
4.6 years ago ahua217 ▴ 10
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1.0k
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How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
4.6 years ago bioinfouser2 ▴ 10
2
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1
reply
2.6k
views
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
4.7 years ago amafon95 ▴ 20
0
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1
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1.2k
views
p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 21 months ago by • 0 • written 4.8 years ago by • 0
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0
replies
1.2k
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
5.0 years ago hfyuan2016 • 0
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0
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1.1k
views
Potential oversimplification in the overlap function
ChIPseeker
5.0 years ago konsta.kukkonen • 0
1
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0
replies
1.2k
views
Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
5.0 years ago egbastakis • 0
0
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1
reply
2.1k
views
ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
5.1 years ago Assa Yeroslaviz ★ 1.5k
0
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1
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1.3k
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ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
5.2 years ago Guandong Shang ▴ 40
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1
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2.0k
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Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
5.7 years ago sutturka • 0
1
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2
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4.2k
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Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
5.7 years ago researcher • 0
2
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1
reply
4.7k
views
Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
5.7 years ago endrebak85 ▴ 40
1
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3
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1.6k
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 5.9 years ago by 25k • written 5.9 years ago by ▴ 20
0
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1
reply
3.3k
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error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
6.0 years ago Theo ▴ 10
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1
reply
1.4k
views
Problem in using covplot ChIPseeker
ChIPseeker software error
6.2 years ago vasudha.sharma • 0
3
votes
2
replies
2.3k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 6.3 years ago by ★ 2.1k • written 6.3 years ago by ▴ 100
1
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1
reply
2.1k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 3.8 years ago by • 0 • written 6.4 years ago by ▴ 10
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0
replies
1.4k
views
How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
6.4 years ago bioinfouser2 ▴ 10
0
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2
replies
1.5k
views
how to get frequencies from plotDistToTSS
chipseeker
6.4 years ago KKO • 0
1
vote
0
replies
1.3k
views
ChipSeeker Flanking gene annotation
chipseeker
6.6 years ago Lauma R ▴ 10
50 results • Page 1 of 1
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Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr by Paul Harrison ▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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