Showing : chippeakanno • reset
22
votes
10
replies
7.4k
views
Error in GRanges: could not find symbol "recursive" in environment of the generic function
granges chippeakanno
updated 7.2 years ago by ▴ 10 • written 7.2 years ago by ▴ 80
9
votes
16
replies
1.7k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
13 months ago • updated 12 months ago Chris • 0
7
votes
9
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1.9k
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counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 3.7 years ago by ★ 4.3k • written 3.7 years ago by ▴ 140
5
votes
15
replies
3.3k
views
nearest genes using TxDb.Hsapiens.UCSC.hg19
txdb.hsapiens.ucsc.hg19.knowngene ChIPpeakAnno
updated 7.9 years ago by ★ 4.3k • written 7.9 years ago by ▴ 140
5
votes
4
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4.7k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r ChIPpeakAnno
7.1 years ago • updated 6.8 years ago salamandra ▴ 20
4
votes
12
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2.6k
views
Curious behaviour of ChIPpeakAnno
chippeakanno
updated 9.5 years ago by ★ 1.3k • written 9.5 years ago by ▴ 20
4
votes
3
replies
1.3k
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 6.9 years ago by ★ 1.3k • written 6.9 years ago by ▴ 110
4
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5
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1.7k
views
ChIPpeakAnno getAnnotation request fail
chippeakanno biomart ensembl
8.3 years ago igor ▴ 40
3
votes
7
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868
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
3
votes
6
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1.6k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
5.8 years ago 94133 • 0
3
votes
5
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3.5k
views
Error with ChIPpeakAnno Ensembl annotation
ChIPpeakAnno genomicfeatures
updated 7.5 years ago by ★ 4.3k • written 7.5 years ago by ▴ 360
2
votes
2
replies
808
views
how to suppress makeVennDiagram plot
ChIPpeakAnno
3.8 years ago C T ▴ 140
2
votes
2
replies
1.6k
views
Can't install ChIPpeakanno - "libmysqlclient was not found" - do I need to remove latest version of R?
ChIPpeakAnno
updated 6.2 years ago by ★ 6.5k • written 6.2 years ago by ▴ 30
2
votes
6
replies
2.2k
views
Problem converting a bed file to granges using togranges chippeakanno
ChIPpeakAnno
updated 2.3 years ago by ▴ 70 • written 2.3 years ago by • 0
2
votes
2
replies
1.3k
views
Hello how to use ChIPpeakAnno for latest version of ensemble genome aligned data
ChIPpeakAnno
3.2 years ago Lucky • 0
2
votes
3
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2.7k
views
org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
chippeakanno annotationdbi
updated 6.5 years ago by • 0 • written 8.5 years ago by • 0
2
votes
7
replies
2.9k
views
ChIPpeakAnno-problem exporting data due to "arguments imply differing number of rows"
chippeakanno
updated 7.4 years ago by ★ 4.3k • written 7.4 years ago by • 0
2
votes
4
replies
1.7k
views
ChIPpeakAnno annotatePeakInBatch output
chippeakanno
8.3 years ago igor ▴ 40
2
votes
10
replies
3.3k
views
ChIPpeakAnno, MACS format annotation
bioconductor ChIPpeakAnno
updated 5.3 years ago by ★ 4.3k • written 7.1 years ago by ▴ 30
2
votes
14
replies
1.1k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 8 months ago by 65k • written 8 months ago by ▴ 10
2
votes
1
reply
1.3k
views
ChIPpeakAnno: Non-empty IRange object in case of no overlap
chippeakanno iranges
updated 9.4 years ago by ★ 4.3k • written 9.4 years ago by ▴ 30
2
votes
3
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1.6k
views
ChIPpeakAnno-annotation of peaklist with gene names, creating heat maps
chippeakanno overlappingpeaks annotation
updated 7.4 years ago by ★ 1.3k • written 7.4 years ago by • 0
1
vote
6
replies
1.4k
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
5.2 years ago ngs06 ▴ 20
1
vote
1
reply
940
views
Custom regions in assignChromosomeRegion?
chippeakanno
updated 6.3 years ago by ★ 1.3k • written 6.3 years ago by • 0
1
vote
2
replies
1.7k
views
another problem when converting bed to granges using togranges
ChIPpeakAnno
2.2 years ago Bakhtiyar • 0
1
vote
1
reply
637
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
21 months ago mehdi • 0
1
vote
5
replies
574
views
ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
6 months ago ilaria.maurizio • 0
1
vote
6
replies
1.5k
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
2.9 years ago Arunima ▴ 10
1
vote
2
replies
2.4k
views
ChIPpeakAnno findOverlapsOfPeaks error: "Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs."
HELP ChIPpeakAnno
2.5 years ago lexi.kellington • 0
1
vote
3
replies
917
views
genomicElementDistribution function not found
ChIPpeakAnno
updated 2.9 years ago by ★ 4.3k • written 2.9 years ago by ▴ 10
1
vote
2
replies
965
views
How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
ChIPpeakAnno
4.8 years ago liruiradiant • 0
1
vote
2
replies
637
views
How to map geneIds to ENTREZIDs
Xenopus_laevis ChIPpeakAnno
15 months ago stacy.genovese • 0
1
vote
2
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2.4k
views
Error : object path is not exported by namespace:Rsamtools
packages installation problem rsamtools chippeakanno ensembldb
6.4 years ago inzirio ▴ 10
1
vote
4
replies
1.5k
views
ChIPpeakAnno binOverGene error
chippeakanno binOverGene
updated 6.4 years ago by ★ 1.3k • written 6.5 years ago by • 0
1
vote
1
reply
964
views
Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap chippeakanno
updated 6.0 years ago by ★ 1.3k • written 6.0 years ago by • 0
1
vote
1
reply
610
views
Interpretation of $vennCounts output "Others"
ChIPpeakAnno
updated 16 months ago by ★ 1.3k • written 16 months ago by ▴ 10
1
vote
9
replies
3.7k
views
ChIPpeakAnno: findOverlapsOfPeaks keep GRanges metadata
chippeakanno findOverlapsOfPeaks
updated 9.0 years ago by ▴ 240 • written 9.0 years ago by ▴ 30
1
vote
1
reply
1.9k
views
ChIP-seq, peak annotation using ChIPpeakAnno
chipseq chippeakanno
updated 8.5 years ago by ★ 1.3k • written 8.5 years ago by • 0
1
vote
1
reply
1.1k
views
Regarding ChIPpeakAnno installation error
chippeakanno
updated 7.0 years ago by 25k • written 7.0 years ago by ▴ 10
1
vote
2
replies
2.0k
views
ChipPeakAnno:getAnnotation using UCSC instead of ensembl
annotation chippeakanno
updated 9.3 years ago by ★ 1.3k • written 9.3 years ago by • 0
0
votes
7
replies
1.9k
views
ChIPpeakAnno::getEnrichedGo crashes but I don't know why
annotate ChIPpeakAnno annotate ChIPpeakAnno
updated 13.3 years ago by ★ 4.3k • written 13.3 years ago by ▴ 40
0
votes
0
replies
846
views
Regarding to ChIPpeakAnno package
ChIPpeakAnno ChIPpeakAnno
13.4 years ago Julie Zhu ★ 4.3k
0
votes
7
replies
1.5k
views
[Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function
Annotation GO BSgenome BSgenome ChIPpeakAnno Annotation GO BSgenome BSgenome ChIPpeakAnno
updated 14.2 years ago by ▴ 310 • written 14.2 years ago by ★ 4.3k
0
votes
0
replies
664
views
A question about outputting GO annotation
Annotation GO ChIPpeakAnno Annotation GO ChIPpeakAnno
13.4 years ago Julie Zhu ★ 4.3k
0
votes
2
replies
1.2k
views
totalTest number in ChipPeakAnno
ChIPpeakAnno ChIPpeakAnno
updated 13.5 years ago by ▴ 30 • written 13.5 years ago by ▴ 410
0
votes
3
replies
1.1k
views
ChIPpeakAnno
Transcription ChIPpeakAnno Transcription ChIPpeakAnno
14.3 years ago • updated 14.2 years ago Julie Zhu ★ 4.3k
0
votes
2
replies
1.5k
views
About ChIPpeakAnno
miRNA ChIPpeakAnno miRNA ChIPpeakAnno
updated 10.1 years ago by ★ 4.3k • written 10.1 years ago by ▴ 330
0
votes
0
replies
759
views
ChIPpeakAnno
ChIPpeakAnno ChIPpeakAnno
13.5 years ago Julie Zhu ★ 4.3k
0
votes
3
replies
1.2k
views
strange ChIPpeakAnno and rtracklayer interaction.
GO annotate rtracklayer ChIPpeakAnno GO annotate rtracklayer ChIPpeakAnno
updated 13.6 years ago by ★ 11k • written 13.6 years ago by ▴ 20
0
votes
0
replies
773
views
[Bioc-devel] BSgenome error
GO BSgenome BSgenome IRanges ChIPpeakAnno GO BSgenome BSgenome IRanges ChIPpeakAnno
14.4 years ago Tony Chiang ▴ 570
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cannot connect to ExperimentHub server by Jiayu • 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea() by Chris • 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
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