Showing : ChIPpeakAnno • reset
1
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Annotation by CHIPeakAnno tool
ChIPpeakAnno
5 weeks ago • updated 4 weeks ago Arunima ▴ 10
1
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3
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112
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genomicElementDistribution function not found
ChIPpeakAnno
updated 5 weeks ago by ★ 4.3k • written 5 weeks ago by ▴ 10
2
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2
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301
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Hello how to use ChIPpeakAnno for latest version of ensemble genome aligned data
ChIPpeakAnno
4 months ago Lucky • 0
7
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9
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460
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counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 11 months ago by ★ 4.3k • written 11 months ago by ▴ 140
2
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2
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171
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how to suppress makeVennDiagram plot
ChIPpeakAnno
11 months ago C T ▴ 140
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2
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244
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How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
ChIPpeakAnno
2.0 years ago liruiradiant • 0
0
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1
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338
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Unable to annotate in ChIPQC using yeast genome
ChIPQC GenomicRanges ChIPpeakAnno
updated 11 weeks ago by • 0 • written 2.2 years ago by • 0
0
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4
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357
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chippeakanno file reading error
ChiPpeakAnno
2.3 years ago saddamhusain77 • 0
1
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6
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387
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how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
2.5 years ago ngs06 ▴ 20
2
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10
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1.4k
views
ChIPpeakAnno, MACS format annotation
bioconductor ChIPpeakAnno
updated 2.5 years ago by ★ 4.3k • written 4.3 years ago by ▴ 30
0
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7
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542
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ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 2.9 years ago by ★ 1.2k • written 2.9 years ago by • 0
3
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6
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692
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ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
3.0 years ago 94133 • 0
0
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1
reply
392
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Error creating pool for permutation test (PeakPermTest)
permutation pool chippeakanno
3.0 years ago ge2sasag • 0
1
vote
1
reply
415
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Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap chippeakanno
updated 3.3 years ago by ★ 1.2k • written 3.3 years ago by • 0
2
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2
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779
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Can't install ChIPpeakanno - "libmysqlclient was not found" - do I need to remove latest version of R?
ChIPpeakAnno
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by ▴ 20
0
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3
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590
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integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno assignChromosomeRegion
updated 3.5 years ago by ★ 4.3k • written 3.5 years ago by ▴ 740
1
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1
reply
416
views
Custom regions in assignChromosomeRegion?
chippeakanno
updated 3.5 years ago by ★ 1.2k • written 3.5 years ago by • 0
1
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2
replies
1.3k
views
Error : object path is not exported by namespace:Rsamtools
packages installation problem rsamtools chippeakanno ensembldb
3.6 years ago inzirio ▴ 10
1
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4
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776
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ChIPpeakAnno binOverGene error
chippeakanno binOverGene
updated 3.7 years ago by ★ 1.2k • written 3.7 years ago by • 0
0
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1
reply
653
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ChIPpeakAnno to find peaks nearest to miRNA
ChIPpeakAnno ChIPpeakAnno
updated 3.8 years ago by • 0 • written 8.6 years ago by ▴ 120
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3
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1.7k
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org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
chippeakanno annotationdbi
updated 3.8 years ago by • 0 • written 5.8 years ago by • 0
0
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1
reply
714
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featureAlignedSignal() error: deparse(sig): object 'sig' not found.
bioconductor chippeakanno featureAlignedDistribution featureAlignedSignal
updated 3.8 years ago by • 0 • written 4.9 years ago by • 0
0
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1
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562
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Help for ChIP script !! Error message while installing packages
annotation chippeakanno
updated 3.8 years ago by 25k • written 3.8 years ago by • 0
5
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4
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2.3k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r ChIPpeakAnno
4.3 years ago • updated 4.0 years ago salamandra • 0
4
votes
3
replies
665
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 4.1 years ago by ★ 1.2k • written 4.1 years ago by ▴ 110
1
vote
1
reply
605
views
Regarding ChIPpeakAnno installation error
chippeakanno
updated 4.2 years ago by 25k • written 4.2 years ago by ▴ 10
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3
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1.2k
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ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is different than output of ol1$overlappingPeaks
chippeakanno
updated 4.3 years ago by ★ 1.2k • written 4.3 years ago by • 0
22
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10
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6.2k
views
Error in GRanges: could not find symbol "recursive" in environment of the generic function
granges chippeakanno
updated 4.4 years ago by ▴ 10 • written 4.4 years ago by ▴ 80
2
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3
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799
views
ChIPpeakAnno-annotation of peaklist with gene names, creating heat maps
chippeakanno overlappingpeaks annotation
updated 4.6 years ago by ★ 1.2k • written 4.6 years ago by • 0
2
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7
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2.0k
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ChIPpeakAnno-problem exporting data due to "arguments imply differing number of rows"
chippeakanno
updated 4.7 years ago by ★ 4.3k • written 4.7 years ago by • 0
3
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5
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1.7k
views
Error with ChIPpeakAnno Ensembl annotation
ChIPpeakAnno genomicfeatures
updated 4.7 years ago by ★ 4.3k • written 4.7 years ago by ▴ 340
0
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1
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466
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Discordant results in finding overlaps for three peak data with ChIPpeakAnno
ChIPpeakAnno
5.0 years ago moyitasha • 0
5
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15
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1.8k
views
nearest genes using TxDb.Hsapiens.UCSC.hg19
txdb.hsapiens.ucsc.hg19.knowngene ChIPpeakAnno
updated 5.1 years ago by ★ 4.3k • written 5.2 years ago by ▴ 140
0
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1
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707
views
Error with findOverlapsOfPeaks
ChIPpeakAnno
5.3 years ago alex.tamburino • 0
0
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3
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884
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CHiPpeakAnno GO and/or KEGG results presenting
chippeakanno go kegg graphics
5.3 years ago lokapal • 0
0
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2
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1.3k
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Help with toGRanges
granges chippeakanno
updated 5.3 years ago by ★ 1.5k • written 5.3 years ago by • 0
0
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0
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766
views
count overlapping reads for CpG islands and annotate with gene names?
annotation chippeakanno rattus norvegicus medip-seq
5.4 years ago Vang Le ▴ 70
2
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4
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794
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ChIPpeakAnno annotatePeakInBatch output
chippeakanno
5.5 years ago igor ▴ 40
4
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5
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927
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ChIPpeakAnno getAnnotation request fail
chippeakanno biomart ensembl
5.5 years ago igor ▴ 40
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2
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1.3k
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Problems installing ChipPeakAnno with newest version of R and Bioconductor
chippeakanno installation
5.7 years ago rebecca.halbach • 0
0
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3
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678
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ChIPpeakAnno (makeVennDiagram) giving different results than before
chippeakanno venn diagram
updated 5.7 years ago by ★ 1.2k • written 5.7 years ago by • 0
1
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1
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1.3k
views
ChIP-seq, peak annotation using ChIPpeakAnno
chipseq chippeakanno
updated 5.7 years ago by ★ 1.2k • written 5.7 years ago by • 0
0
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0
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663
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Different amount of overlapping Peaks in ChIPpeakAnno-Package
chippeakanno findoverlaps venn diagram
5.7 years ago N. F. • 0
0
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0
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580
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No genes' ID in peak annotations during ChiP-Seq with ChIPpeakAnno R package
chippeakanno chipseq annotation
5.8 years ago MarcinKosiński • 0
1
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9
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2.4k
views
ChIPpeakAnno: findOverlapsOfPeaks keep GRanges metadata
chippeakanno findOverlapsOfPeaks
updated 6.2 years ago by ▴ 240 • written 6.2 years ago by ▴ 20
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1
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1.3k
views
Scaled venn/euler diagram using makeVennDiagram
ChIPpeakAnno venn diagram
updated 6.2 years ago by ★ 1.2k • written 6.2 years ago by ▴ 20
0
votes
2
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976
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News: ChIPpeakAnno::getAnnotation get Exons
chippeakanno News
updated 6.4 years ago by ★ 1.2k • written 6.4 years ago by ★ 4.3k
0
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1
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1.2k
views
Error attaching GO.db package
GO.db loadnamespace annotation chippeakanno
updated 6.4 years ago by ★ 8.2k • written 6.4 years ago by • 0
0
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5
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659
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Get ChIPpeakAnno to report total number of covered bases in VennDiagrams instead of (or in addition to) regions
chippeakanno
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by ▴ 20
1
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2
replies
1.4k
views
ChipPeakAnno:getAnnotation using UCSC instead of ensembl
annotation chippeakanno
updated 6.6 years ago by ★ 1.2k • written 6.6 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: featureCounts - paired-end data by Yanfang • 0
Hey Wei shi, May I ask you something related to featureCounts? I have only paired end reads (RNAseq) mapping to its genome by bowtie2, an…
Comment: WGCNA adjust p value by Kevin Blighe 3.2k
Cross-posted: https://www.biostars.org/p/9482927/
Comment: Unique GPos taking into account mcols by Marcel Ramos 540
Hi @maltethodberg We currently do not have a method that does this. Perhaps a `duplicated` method is appropriate but I am not the develop…
Comment: What are these genes ? [How to get Ensembl IDs for them] by abf ▴ 30
Mouse genes are not typically all capitals, but I was able to find a reference to a mouse gene in NCBI to [CH36-217G15][1]. Maybe this is …
Comment: Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db. by abf ▴ 30
I should note that when I query org.Mm.eg.db using the gene Symbols associated with my differential expression data I find a 1:1 correspond…
Votes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
A: Normalized counts of DESeq2 affected by design formula?
A: Finding orthologous human/mouse ENSEMBL IDs
Comment: What are these genes ? [How to get Ensembl IDs for them]
Answer: What lfcSE is dependent upon?
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