Showing : chiPseeker • reset
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ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
6 months ago Anton01 • 0
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233
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[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
7 months ago Henry ▴ 10
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1
reply
522
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plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 12 months ago by 67k • written 12 months ago by • 0
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2
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908
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annotatePeak error for some problem
ChIPseeker
written 12 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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742
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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
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1
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1.1k
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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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4.8k
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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 23 months ago by 67k • written 23 months ago by • 0
1
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857
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Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
2.3 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
2.4 years ago Palmira • 0
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2.7k
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How to define 'distal intergenic'
ChIPseeker
2.5 years ago Sanghoon • 0
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1
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1.2k
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ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
2.5 years ago Gyan Prakash Mishra ▴ 10
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0
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860
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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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907
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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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1.9k
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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
3.1 years ago guoyou88 • 0
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0
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924
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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
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what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
3.4 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
3.5 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 3.6 years ago by ▴ 10 • written 3.6 years ago by ▴ 10
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0
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999
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What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
3.6 years ago Sam ▴ 10
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0
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1.2k
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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
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ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
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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886
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ChIPSeeker covplot function, fix yaxis
ChIPseeker
3.8 years ago jordi.planells • 0
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0
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887
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Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
4.0 years ago Sam ▴ 10
2
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2
replies
2.7k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
4.0 years ago • updated 3.8 years ago Mar Mar ▴ 20
5
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3
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2.0k
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importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 4.0 years ago by 67k • written 4.0 years ago by ▴ 10
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0
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744
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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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1.8k
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
4.1 years ago ahua217 ▴ 10
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0
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899
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How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
4.1 years ago bioinfouser2 ▴ 10
2
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1
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2.2k
views
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
4.2 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 4.3 years ago by • 0
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0
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1.1k
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ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
4.5 years ago hfyuan2016 • 0
0
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0
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934
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
4.6 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
0
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1
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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
5.2 years ago researcher • 0
2
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1
reply
4.2k
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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
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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 5.4 years ago by 25k • written 5.4 years ago by ▴ 10
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1
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3.0k
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
5.7 years ago vasudha.sharma • 0
3
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2
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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
5.9 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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Answer: What type of counts data to import for performing Isoform analysis in edgeR by Gordon Smyth 52k
I haven't used nf-core but, from browsing through their documentation, they didn't seem to have any pipeline for differential transcript ex…
Comment: What type of counts data to import for performing Isoform analysis in edgeR by Gordon Smyth 52k
The poster needs to run Salmon with `--numGibbsSamples=50`. I suspect that nf-core just won't do that, so Salmon needs to be run directly.
Comment: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.6k
Probably nf-core did not run with bootstrap/gibbs replicates. Check the code. See salmon docs on how to turn that on.
Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10
@atpoint Thank you. I did wanted to try using the `quant.sf` files from the `salmon` run by referring edgeR user guide example `4.6 Differe…
Comment: athPkgBuilder data source :missing probesets by bobihanigujjar • 0
In this article, we'll explore the demand for unbranded BJJ Gis and the benefits of choosing unbranded Gis for customization. [does anyone …
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Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
Comment: ANOVA like approach of edgeR
Comment: Crossover design with limma
Answer: DESeq2 normalization vs VST vs rlog
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