Showing : Chipseeker • reset
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[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
18 days ago Henry ▴ 10
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1
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311
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plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 5 months ago by 65k • written 5 months ago by • 0
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1
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380
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annotatePeak error for some problem
ChIPseeker
updated 5 months ago by 65k • written 5 months ago by • 0
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2
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1.0k
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how i can get the name of genes in pathway?
chipseq ChIPseeker
14 months ago chavaleab • 0
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0
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570
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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
14 months ago 840842906 • 0
0
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1
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818
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Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 15 months ago by 65k • written 15 months ago by ▴ 50
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2
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3.2k
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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 16 months ago by 65k • written 16 months ago by • 0
1
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644
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Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
21 months ago arisarkar88 ▴ 40
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0
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791
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
22 months ago Palmira • 0
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0
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1.9k
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How to define 'distal intergenic'
ChIPseeker
23 months ago Sanghoon • 0
0
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1
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970
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ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
23 months ago Gyan Prakash Mishra ▴ 10
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0
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691
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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
2.0 years ago Swadha • 0
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0
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710
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What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
2.1 years ago hyjforesight • 0
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1
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1.6k
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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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2
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982
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getPromoters
ChIPseeker
2.5 years ago guoyou88 • 0
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0
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730
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ChIPseeker, how to customize plotDistToTSS
ChIPseeker
2.6 years ago alexandre.blais ▴ 50
1
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3
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891
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what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
2.9 years ago Meghna • 0
0
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0
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812
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CHIPseeker- promoter gene names
ChIPseeker CHIPsee
2.9 years ago rb • 0
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1
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1.4k
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ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 3.0 years ago by ▴ 10 • written 3.1 years ago by ▴ 10
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0
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839
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What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
3.1 years ago Sam ▴ 10
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0
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1.1k
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Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
3.1 years ago Xiaojie Cheng • 0
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2
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1.0k
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ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
3.1 years ago Onur Karakaslar • 0
1
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4
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2.0k
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Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
3.2 years ago Kasit • 0
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0
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687
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ChIPSeeker covplot function, fix yaxis
ChIPseeker
3.3 years ago jordi.planells • 0
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0
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740
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Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
3.4 years ago Sam ▴ 10
2
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2
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2.4k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
3.5 years ago • updated 3.2 years ago Mar Mar ▴ 20
5
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3
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1.3k
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importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 3.5 years ago by 65k • written 3.5 years ago by ▴ 10
0
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0
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631
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Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
3.5 years ago Prasoon • 0
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1
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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
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0
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894
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About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
3.6 years ago ahua217 ▴ 10
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0
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767
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How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
3.6 years ago bioinfouser2 ▴ 10
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1
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1.8k
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ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
3.7 years ago amafon95 • 0
0
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1
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888
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p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 9 months ago by • 0 • written 3.8 years ago by • 0
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0
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861
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ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
4.0 years ago hfyuan2016 • 0
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0
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742
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Potential oversimplification in the overlap function
ChIPseeker
4.0 years ago konsta.kukkonen • 0
1
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0
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878
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Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
4.0 years ago egbastakis • 0
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1
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1.6k
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ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
4.1 years ago Assa Yeroslaviz ★ 1.5k
0
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1
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1.0k
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ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
4.2 years ago Guandong Shang ▴ 40
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1
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1.6k
views
Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
4.6 years ago sutturka • 0
1
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2
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3.7k
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Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
4.6 years ago researcher • 0
2
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1
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3.6k
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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
1
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3
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1.1k
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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
0
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1
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2.6k
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error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
5.0 years ago Theo ▴ 10
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1
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1.1k
views
Problem in using covplot ChIPseeker
ChIPseeker software error
5.1 years ago vasudha.sharma • 0
3
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2
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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
1
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1
reply
1.7k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 2.8 years ago by • 0 • written 5.3 years ago by ▴ 10
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0
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1.1k
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How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
5.4 years ago bioinfouser2 ▴ 10
0
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2
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1.2k
views
how to get frequencies from plotDistToTSS
chipseeker
5.4 years ago KKO • 0
1
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0
replies
1.0k
views
ChipSeeker Flanking gene annotation
chipseeker
5.6 years ago Lauma R ▴ 10
3
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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
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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