Showing : Chipseeker • reset
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how i can get the name of genes in pathway?
chipseq ChIPseeker
6 months ago chavaleab • 0
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0
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294
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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
6 months ago 840842906 • 0
0
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1
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379
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Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 7 months ago by 63k • written 7 months ago by ▴ 50
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2
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1.9k
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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 9 months ago by 63k • written 9 months ago by • 0
1
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0
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381
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Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
13 months ago arisarkar88 ▴ 40
0
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0
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453
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
14 months ago Palmira • 0
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0
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1.2k
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How to define 'distal intergenic'
ChIPseeker
15 months ago Sanghoon • 0
0
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1
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681
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ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
16 months ago Gyan Prakash Mishra ▴ 10
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0
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449
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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
17 months ago Swadha • 0
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0
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497
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What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
18 months ago hyjforesight • 0
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1
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1.3k
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ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
22 months ago william.ho • 0
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2
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739
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getPromoters
ChIPseeker
23 months ago guoyou88 • 0
0
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0
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544
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ChIPseeker, how to customize plotDistToTSS
ChIPseeker
23 months ago alexandre.blais ▴ 50
1
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3
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646
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what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
2.2 years ago Meghna • 0
0
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0
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589
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CHIPseeker- promoter gene names
ChIPseeker CHIPsee
2.3 years ago rb • 0
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1
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963
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ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 2.4 years ago by ▴ 10 • written 2.4 years ago by ▴ 10
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0
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618
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What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
2.4 years ago Sam ▴ 10
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0
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800
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Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
2.5 years ago Xiaojie Cheng • 0
0
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2
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792
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ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
2.5 years ago Onur Karakaslar • 0
1
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4
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1.4k
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Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
2.6 years ago Kasit • 0
0
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0
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492
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ChIPSeeker covplot function, fix yaxis
ChIPseeker
2.7 years ago jordi.planells • 0
0
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0
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569
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Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
2.8 years ago Sam ▴ 10
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2
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2.0k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
2.9 years ago • updated 2.6 years ago Mar Mar ▴ 20
5
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3
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956
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importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 2.9 years ago by 63k • written 2.9 years ago by ▴ 10
0
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0
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461
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Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
2.9 years ago Prasoon • 0
0
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1
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1.1k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 2.9 years ago by 63k • written 2.9 years ago by • 0
0
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0
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684
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About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
2.9 years ago ahua217 ▴ 10
0
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0
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596
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How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
3.0 years ago bioinfouser2 ▴ 10
0
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1
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1.4k
views
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
3.1 years ago amafon95 • 0
0
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1
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662
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p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 7 weeks ago by • 0 • written 3.1 years ago by • 0
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0
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640
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ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
3.3 years ago hfyuan2016 • 0
0
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0
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544
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Potential oversimplification in the overlap function
ChIPseeker
3.4 years ago konsta.kukkonen • 0
1
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0
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677
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Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
3.4 years ago egbastakis • 0
0
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1
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1.3k
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ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
3.5 years ago Assa Yeroslaviz ★ 1.5k
0
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1
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815
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ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
3.6 years ago Guandong Shang ▴ 40
0
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1
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1.2k
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Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
4.0 years ago sutturka • 0
1
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2
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3.2k
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Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
4.0 years ago researcher • 0
2
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1
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2.8k
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Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
4.1 years ago endrebak85 ▴ 30
1
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3
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885
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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 4.2 years ago by 25k • written 4.2 years ago by ▴ 10
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1
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2.1k
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error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
4.4 years ago Theo • 0
0
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1
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871
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Problem in using covplot ChIPseeker
ChIPseeker software error
4.5 years ago vasudha.sharma • 0
3
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2
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1.4k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 4.6 years ago by ★ 2.0k • written 4.6 years ago by ▴ 80
1
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1
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1.4k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 2.2 years ago by • 0 • written 4.7 years ago by ▴ 10
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0
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956
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How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
4.7 years ago bioinfouser2 ▴ 10
0
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2
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977
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how to get frequencies from plotDistToTSS
chipseeker
4.8 years ago KKO • 0
1
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0
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794
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ChipSeeker Flanking gene annotation
chipseeker
5.0 years ago Lauma R ▴ 10
3
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4
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1.9k
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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 5.0 years ago by 63k • written 5.0 years ago by • 0
0
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0
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667
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covplot and getChrCov function
chipseeker
5.0 years ago xiaofeiwang198266 • 0
1
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3
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1.3k
views
How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 5.0 years ago by ★ 1.2k • written 5.1 years ago by ▴ 10
0
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0
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733
views
How to get the genome distribution in proportion of promoter, 1st exon, other exon, 1st intron, other intron, distal intergenic, etc from a species
chipseeker
5.1 years ago bright602 • 0
50 results • Page 1 of 1
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Answer: ukb Chromosomal position information was converted into SNPS by James W. MacDonald 63k
In my work, we almost always convert RSIDs to chr:pos because the former is ambiguous and changing whereas the latter is not. Which is like…
Comment: T.fit function of maSigPro returns error message by hanna.g • 0
Addition to the issue above: the T.fit function works only when choosing the step.method = "forward", for whatever reason. Maybe this clue …
Answer: Deseq2, enrichGO and ensembl ID by James W. MacDonald 63k
1. There isn't a keytype alternative. You need the gene IDs. 2. Convert the `rownames` of your 'se' object, or the `rownames` of your `D…
Comment: Doubts regarding Pathview by loyedbend2811 • 0
I thoroughly enjoyed reading your essay, and it was quite beneficial to me. Please join me in [monopoly online][1] if you have the time. …
Comment: ukb Chromosomal position information was converted into SNPS by wenbo • 0
Hi, I downloaded uk biobank data, but I don't know how to use R to convert chromosome position information to rs
Votes
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
Comment: comparing contrasts in edger/lima using makeContrasts function
Answer: comparing contrasts in edger/lima using makeContrasts function
Answer: Differential expression analysis with only FPKM matrix available from total newb
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