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ChIPpeakAnno
•
reset
9
votes
16
replies
1.6k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
11 months ago
Chris
• 0
5
votes
15
replies
3.3k
views
nearest genes using TxDb.Hsapiens.UCSC.hg19
txdb.hsapiens.ucsc.hg19.knowngene
ChIPpeakAnno
updated 7.8 years ago by
Julie Zhu
★ 4.3k • written 7.8 years ago by
C T
▴ 140
2
votes
14
replies
1.0k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno
ChIPSeq
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
Jerina
▴ 10
4
votes
12
replies
2.5k
views
Curious behaviour of ChIPpeakAnno
chippeakanno
updated 9.4 years ago by
Ou, Jianhong
★ 1.3k • written 9.4 years ago by
Brad Davis
▴ 20
0
votes
12
replies
2.4k
views
more stupid *Ranges questions...
Transcription
ChIPpeakAnno
GenomicRanges
Transcription
ChIPpeakAnno
GenomicRanges
updated 12.5 years ago by
Michael Lawrence
★ 11k • written 12.5 years ago by
Tim Triche
★ 4.2k
2
votes
10
replies
3.2k
views
ChIPpeakAnno, MACS format annotation
bioconductor
ChIPpeakAnno
updated 5.2 years ago by
Julie Zhu
★ 4.3k • written 7.0 years ago by
Khademul Islam
▴ 30
22
votes
10
replies
7.4k
views
Error in GRanges: could not find symbol "recursive" in environment of the generic function
granges
chippeakanno
updated 7.0 years ago by
davide.porcellato
▴ 10 • written 7.1 years ago by
deut13
▴ 80
1
vote
9
replies
3.6k
views
ChIPpeakAnno: findOverlapsOfPeaks keep GRanges metadata
chippeakanno
findOverlapsOfPeaks
updated 8.8 years ago by
Hari Easwaran
▴ 240 • written 8.9 years ago by
da.de
▴ 30
7
votes
9
replies
1.8k
views
counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 3.6 years ago by
Julie Zhu
★ 4.3k • written 3.6 years ago by
C T
▴ 140
0
votes
8
replies
1.6k
views
ChIPpeakAnno Strandedness and distance calculation
Annotation
Cancer
ChIPpeakAnno
Annotation
Cancer
ChIPpeakAnno
updated 13.9 years ago by
Dario Strbenac
★ 1.5k • written 13.9 years ago by
Julie Zhu
★ 4.3k
0
votes
7
replies
1.9k
views
ChIPpeakAnno::getEnrichedGo crashes but I don't know why
annotate
ChIPpeakAnno
annotate
ChIPpeakAnno
updated 13.2 years ago by
Julie Zhu
★ 4.3k • written 13.2 years ago by
Eric Cabot
▴ 40
3
votes
7
replies
792
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 6 months ago by
Chris
• 0
2
votes
7
replies
2.9k
views
ChIPpeakAnno-problem exporting data due to "arguments imply differing number of rows"
chippeakanno
updated 7.3 years ago by
Julie Zhu
★ 4.3k • written 7.3 years ago by
jmKeith
• 0
0
votes
7
replies
1.4k
views
[Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function
Annotation
GO
BSgenome
BSgenome
ChIPpeakAnno
Annotation
GO
BSgenome
BSgenome
ChIPpeakAnno
updated 14.1 years ago by
Ivan Gregoretti
▴ 310 • written 14.1 years ago by
Julie Zhu
★ 4.3k
0
votes
7
replies
1.5k
views
ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno
chipseq
R
updated 5.5 years ago by
Ou, Jianhong
★ 1.3k • written 5.5 years ago by
94133
• 0
0
votes
7
replies
1.4k
views
Problem loading BED file with BED2RangedData
GO
ChIPpeakAnno
GO
ChIPpeakAnno
updated 11.3 years ago by
Ou, Jianhong
★ 1.3k • written 11.3 years ago by
José Luis Lavín
▴ 280
2
votes
6
replies
2.0k
views
Problem converting a bed file to granges using togranges chippeakanno
ChIPpeakAnno
updated 2.1 years ago by
Kai Hu
▴ 70 • written 2.1 years ago by
Bakhtiyar
• 0
3
votes
6
replies
1.6k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq
chippeakanno
chipseeker
5.7 years ago
94133
• 0
1
vote
6
replies
1.5k
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
2.8 years ago
Arunima
▴ 10
0
votes
6
replies
1.5k
views
Question RE: getEnrichedGo in ChIPpeakAnno package
Yeast
ChIPpeakAnno
Starr
Yeast
ChIPpeakAnno
Starr
updated 13.8 years ago by
Julie Zhu
★ 4.3k • written 13.8 years ago by
Noah Dowell
▴ 410
1
vote
6
replies
1.3k
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
5.1 years ago
ngs06
▴ 20
0
votes
5
replies
1.2k
views
Get ChIPpeakAnno to report total number of covered bases in VennDiagrams instead of (or in addition to) regions
chippeakanno
updated 9.2 years ago by
Ou, Jianhong
★ 1.3k • written 9.2 years ago by
Brad Davis
▴ 20
3
votes
5
replies
3.5k
views
Error with ChIPpeakAnno Ensembl annotation
ChIPpeakAnno
genomicfeatures
updated 7.4 years ago by
Julie Zhu
★ 4.3k • written 7.4 years ago by
b.nota
▴ 360
0
votes
5
replies
1.1k
views
ChIPpeakAnno question--peak aggregation over bins from TSS
ChIPpeakAnno
ChIPpeakAnno
updated 11.2 years ago by
Julie Zhu
★ 4.3k • written 11.2 years ago by
kamesh
▴ 40
0
votes
5
replies
1.4k
views
Query on ChipPeakAnno: AnnotatePeakinBatch input
Annotation
Cancer
ChIPpeakAnno
Annotation
Cancer
ChIPpeakAnno
updated 10.3 years ago by
Jailwala, Parthav NIH/NCI [C]
▴ 30 • written 10.3 years ago by
Julie Zhu
★ 4.3k
4
votes
5
replies
1.7k
views
ChIPpeakAnno getAnnotation request fail
chippeakanno
biomart
ensembl
8.2 years ago
igor
▴ 40
1
vote
5
replies
481
views
ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
5 months ago
ilaria.maurizio
• 0
0
votes
5
replies
1.5k
views
[ChIPpeakAnno] Can not start ChIPpeakAnno after update to version 2.5.9
ChIPpeakAnno
ChIPpeakAnno
updated 11.8 years ago by
Steve Lianoglou
★ 13k • written 11.8 years ago by
sheng zhao
▴ 90
0
votes
4
replies
1.2k
views
ChIPpeakAnno
convert
ChIPpeakAnno
convert
ChIPpeakAnno
11.6 years ago
Julie Zhu
★ 4.3k
1
vote
4
replies
1.5k
views
ChIPpeakAnno binOverGene error
chippeakanno
binOverGene
updated 6.3 years ago by
Ou, Jianhong
★ 1.3k • written 6.3 years ago by
Wojeff
• 0
5
votes
4
replies
4.6k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r
ChIPpeakAnno
7.0 years ago • updated 6.7 years ago
salamandra
▴ 20
0
votes
4
replies
1.2k
views
more question about makeVennDiagram
GO
ChIPpeakAnno
GO
ChIPpeakAnno
11.7 years ago
Julie Zhu
★ 4.3k
0
votes
4
replies
1.3k
views
about ChIPpeakAnno
Annotation
ChIPpeakAnno
Annotation
ChIPpeakAnno
13.5 years ago
Julie Zhu
★ 4.3k
0
votes
4
replies
1.2k
views
question regarding ChIPPeakAnno use
ChIPpeakAnno
ChIPpeakAnno
updated 12.0 years ago by
Ma, Xian-Yong
▴ 20 • written 12.0 years ago by
Julie Zhu
★ 4.3k
0
votes
4
replies
1.1k
views
Suggestion for a small change to ChIPpeakAnno
ChIPpeakAnno
ChIPpeakAnno
9.7 years ago
Julie Zhu
★ 4.3k
0
votes
4
replies
2.1k
views
ChIPpeakAnno as.data.frame error
GO
AnnotationData
annotate
convert
ChIPpeakAnno
GO
AnnotationData
annotate
convert
updated 12.1 years ago by
Julie Zhu
★ 4.3k • written 12.1 years ago by
Mark Cowley
▴ 910
0
votes
4
replies
2.0k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
2.4 years ago
Tongjun
• 0
0
votes
4
replies
1.2k
views
chippeakanno file reading error
ChiPpeakAnno
5.0 years ago
saddamhusain77
• 0
2
votes
4
replies
1.6k
views
ChIPpeakAnno annotatePeakInBatch output
chippeakanno
8.2 years ago
igor
▴ 40
0
votes
3
replies
1.1k
views
ChipPeakAnno - slightly different results between makeVennDiagram and findPeakOverlaps
Genetics
ChIPpeakAnno
Genetics
ChIPpeakAnno
updated 11.5 years ago by
Ou, Jianhong
★ 1.3k • written 11.5 years ago by
António Miguel de Jesus Domingues
▴ 490
0
votes
3
replies
1.0k
views
ChIPpeakAnno
Transcription
ChIPpeakAnno
Transcription
ChIPpeakAnno
14.2 years ago • updated 14.1 years ago
Julie Zhu
★ 4.3k
4
votes
3
replies
1.3k
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 6.8 years ago by
Ou, Jianhong
★ 1.3k • written 6.8 years ago by
Haiying.Kong
▴ 110
0
votes
3
replies
1.1k
views
strange ChIPpeakAnno and rtracklayer interaction.
GO
annotate
rtracklayer
ChIPpeakAnno
GO
annotate
rtracklayer
ChIPpeakAnno
updated 13.4 years ago by
Michael Lawrence
★ 11k • written 13.4 years ago by
oleg@stat.berkeley.edu
▴ 20
0
votes
3
replies
2.4k
views
ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is different than output of ol1$overlappingPeaks
chippeakanno
updated 7.0 years ago by
Ou, Jianhong
★ 1.3k • written 7.0 years ago by
sudhirjadhao2009
• 0
0
votes
3
replies
1.1k
views
RE ChIPPEAKANNO
miRNA
Genetics
ChIPpeakAnno
miRNA
Genetics
ChIPpeakAnno
11.6 years ago
Julie Zhu
★ 4.3k
0
votes
3
replies
1.7k
views
ChIPpeakAnno to find peaks nearest to miRNA
miRNA
GO
BSgenome
BSgenome
ChIPpeakAnno
miRNA
GO
BSgenome
BSgenome
ChIPpeakAnno
updated 11.7 years ago by
Julie Zhu
★ 4.3k • written 11.7 years ago by
Paolo Kunderfranco
▴ 350
0
votes
3
replies
1.3k
views
ChIPpeakAnno problem w getAllPeakSequence()
GO
annotate
ChIPpeakAnno
GO
annotate
ChIPpeakAnno
updated 11.5 years ago by
Ou, Jianhong
★ 1.3k • written 11.5 years ago by
Anna
▴ 50
0
votes
3
replies
1.3k
views
integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno
assignChromosomeRegion
updated 6.1 years ago by
Julie Zhu
★ 4.3k • written 6.1 years ago by
Janet Young
▴ 740
0
votes
3
replies
1.2k
views
chippeakanno:::addGeneID for adding gene symbol etc. to annotatedPeak or enrichedGO
Annotation
convert
biomaRt
bridge
ChIPpeakAnno
Annotation
convert
biomaRt
bridge
updated 12.6 years ago by
Andreia Fonseca
▴ 810 • written 12.7 years ago by
Julie Zhu
★ 4.3k
0
votes
3
replies
945
views
ChIPpeakAnno 2.12.2 bug
ChIPpeakAnno
ChIPpeakAnno
updated 9.6 years ago by
Ou, Jianhong
★ 1.3k • written 9.6 years ago by
Julie Zhu
★ 4.3k
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