Showing : chiPseeker • reset
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ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
7 months ago Anton01 • 0
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0
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245
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[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
8 months ago Henry ▴ 10
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1
reply
536
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plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 13 months ago by 67k • written 13 months ago by • 0
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2
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964
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annotatePeak error for some problem
ChIPseeker
written 13 months ago by • 0
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2
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1.4k
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how i can get the name of genes in pathway?
chipseq ChIPseeker
21 months ago chavaleab • 0
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0
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768
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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
21 months ago 840842906 • 0
0
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1
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1.2k
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Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 22 months ago by 67k • written 22 months ago by ▴ 50
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2
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5.0k
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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 24 months ago by 67k • written 24 months ago by • 0
1
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876
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Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
2.4 years ago arisarkar88 ▴ 40
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1.0k
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
2.5 years ago Palmira • 0
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2.8k
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How to define 'distal intergenic'
ChIPseeker
2.5 years ago Sanghoon • 0
0
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1
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1.3k
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ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
2.6 years ago Gyan Prakash Mishra ▴ 10
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0
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873
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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
2.6 years ago Swadha • 0
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0
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923
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What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
2.7 years ago hyjforesight • 0
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1
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2.0k
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ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
3.1 years ago william.ho • 0
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2
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1.3k
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getPromoters
ChIPseeker
3.2 years ago guoyou88 • 0
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0
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935
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ChIPseeker, how to customize plotDistToTSS
ChIPseeker
3.2 years ago alexandre.blais ▴ 50
1
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3
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1.1k
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
3.5 years ago Meghna • 0
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0
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1.0k
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CHIPseeker- promoter gene names
ChIPseeker CHIPsee
3.6 years ago rb • 0
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1
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1.7k
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ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 3.7 years ago by ▴ 10 • written 3.7 years ago by ▴ 10
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0
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1.0k
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What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
3.7 years ago Sam ▴ 10
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0
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1.3k
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Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
3.7 years ago Xiaojie Cheng • 0
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2
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1.2k
views
ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
3.8 years ago • updated 3.7 years ago Onur Karakaslar • 0
1
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4
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2.6k
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Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
3.8 years ago Kasit • 0
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0
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895
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ChIPSeeker covplot function, fix yaxis
ChIPseeker
3.9 years ago jordi.planells • 0
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0
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898
views
Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
4.1 years ago • updated 4.0 years ago Sam ▴ 10
2
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2
replies
2.8k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
4.1 years ago • updated 3.9 years ago Mar Mar ▴ 20
5
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3
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2.1k
views
importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 4.1 years ago by 67k • written 4.1 years ago by ▴ 10
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0
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751
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Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
4.1 years ago Prasoon • 0
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1
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1.9k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 4.1 years ago by 67k • written 4.1 years ago by • 0
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0
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1.1k
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About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
4.2 years ago ahua217 ▴ 10
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0
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910
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How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
4.2 years ago bioinfouser2 ▴ 10
2
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1
reply
2.3k
views
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
4.3 years ago amafon95 ▴ 20
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1
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1.1k
views
p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 16 months ago by • 0 • written 4.4 years ago by • 0
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0
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1.1k
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
4.6 years ago hfyuan2016 • 0
0
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0
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948
views
Potential oversimplification in the overlap function
ChIPseeker
4.6 years ago konsta.kukkonen • 0
1
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0
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1.0k
views
Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
4.6 years ago egbastakis • 0
0
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1
reply
1.9k
views
ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
4.7 years ago Assa Yeroslaviz ★ 1.5k
0
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1
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1.2k
views
ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
4.8 years ago Guandong Shang ▴ 40
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1
reply
1.8k
views
Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
5.2 years ago sutturka • 0
1
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2
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4.0k
views
Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
5.3 years ago researcher • 0
2
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1
reply
4.3k
views
Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
5.3 years ago endrebak85 ▴ 40
1
vote
3
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1.4k
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 5.5 years ago by 25k • written 5.5 years ago by ▴ 10
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1
reply
3.1k
views
error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
5.6 years ago Theo ▴ 10
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1
reply
1.3k
views
Problem in using covplot ChIPseeker
ChIPseeker software error
5.8 years ago vasudha.sharma • 0
3
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2
replies
2.1k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 5.8 years ago by ★ 2.1k • written 5.8 years ago by ▴ 100
1
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1
reply
2.0k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 3.4 years ago by • 0 • written 5.9 years ago by ▴ 10
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0
replies
1.3k
views
How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
6.0 years ago bioinfouser2 ▴ 10
0
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2
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1.4k
views
how to get frequencies from plotDistToTSS
chipseeker
6.0 years ago KKO • 0
1
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0
replies
1.2k
views
ChipSeeker Flanking gene annotation
chipseeker
6.2 years ago Lauma R ▴ 10
50 results • Page 1 of 1
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Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200
Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k
Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…
Votes
Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
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