Showing : ChIPpeakAnno • reset
5
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nearest genes using TxDb.Hsapiens.UCSC.hg19
txdb.hsapiens.ucsc.hg19.knowngene ChIPpeakAnno
updated 6.0 years ago by ★ 4.3k • written 6.1 years ago by ▴ 140
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more stupid *Ranges questions...
Transcription ChIPpeakAnno GenomicRanges Transcription ChIPpeakAnno GenomicRanges
updated 10.8 years ago by 11k • written 10.8 years ago by ★ 4.2k
4
votes
12
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1.7k
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Curious behaviour of ChIPpeakAnno
chippeakanno
updated 7.6 years ago by ★ 1.3k • written 7.6 years ago by ▴ 20
22
votes
10
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views
Error in GRanges: could not find symbol "recursive" in environment of the generic function
granges chippeakanno
updated 5.3 years ago by ▴ 10 • written 5.3 years ago by ▴ 80
2
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10
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1.9k
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ChIPpeakAnno, MACS format annotation
bioconductor ChIPpeakAnno
updated 3.4 years ago by ★ 4.3k • written 5.2 years ago by ▴ 30
1
vote
9
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views
ChIPpeakAnno: findOverlapsOfPeaks keep GRanges metadata
chippeakanno findOverlapsOfPeaks
updated 7.1 years ago by ▴ 240 • written 7.1 years ago by ▴ 20
7
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9
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773
views
counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 22 months ago by ★ 4.3k • written 22 months ago by ▴ 140
0
votes
8
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892
views
ChIPpeakAnno Strandedness and distance calculation
Annotation Cancer ChIPpeakAnno Annotation Cancer ChIPpeakAnno
updated 12.1 years ago by ★ 1.5k • written 12.1 years ago by ★ 4.3k
0
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7
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713
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ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 3.8 years ago by ★ 1.3k • written 3.8 years ago by • 0
0
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7
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1.5k
views
ChIPpeakAnno::getEnrichedGo crashes but I don't know why
annotate ChIPpeakAnno annotate ChIPpeakAnno
updated 11.5 years ago by ★ 4.3k • written 11.5 years ago by ▴ 40
0
votes
7
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917
views
[Bioc-sig-seq] ChIPpeakAnno annotatePeakInBatch function
Annotation GO BSgenome BSgenome ChIPpeakAnno Annotation GO BSgenome BSgenome ChIPpeakAnno
updated 12.3 years ago by ▴ 310 • written 12.3 years ago by ★ 4.3k
0
votes
7
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views
Problem loading BED file with BED2RangedData
GO ChIPpeakAnno GO ChIPpeakAnno
updated 9.6 years ago by ★ 1.3k • written 9.6 years ago by ▴ 280
2
votes
7
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2.3k
views
ChIPpeakAnno-problem exporting data due to "arguments imply differing number of rows"
chippeakanno
updated 5.5 years ago by ★ 4.3k • written 5.5 years ago by • 0
0
votes
6
replies
974
views
Question RE: getEnrichedGo in ChIPpeakAnno package
Yeast ChIPpeakAnno Starr Yeast ChIPpeakAnno Starr
updated 12.0 years ago by ★ 4.3k • written 12.0 years ago by ▴ 410
2
votes
6
replies
499
views
Problem converting a bed file to granges using togranges chippeakanno
ChIPpeakAnno
updated 4 months ago by ▴ 50 • written 4 months ago by • 0
1
vote
6
replies
593
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
12 months ago Arunima ▴ 10
1
vote
6
replies
531
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
3.3 years ago ngs06 ▴ 20
3
votes
6
replies
857
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
3.9 years ago 94133 • 0
0
votes
5
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755
views
Get ChIPpeakAnno to report total number of covered bases in VennDiagrams instead of (or in addition to) regions
chippeakanno
updated 7.4 years ago by ★ 1.3k • written 7.4 years ago by ▴ 20
0
votes
5
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731
views
ChIPpeakAnno question--peak aggregation over bins from TSS
ChIPpeakAnno ChIPpeakAnno
updated 9.4 years ago by ★ 4.3k • written 9.4 years ago by ▴ 40
0
votes
5
replies
1.0k
views
Query on ChipPeakAnno: AnnotatePeakinBatch input
Annotation Cancer ChIPpeakAnno Annotation Cancer ChIPpeakAnno
updated 8.6 years ago by ▴ 30 • written 8.6 years ago by ★ 4.3k
4
votes
5
replies
1.2k
views
ChIPpeakAnno getAnnotation request fail
chippeakanno biomart ensembl
6.4 years ago igor ▴ 40
3
votes
5
replies
2.2k
views
Error with ChIPpeakAnno Ensembl annotation
ChIPpeakAnno genomicfeatures
updated 5.6 years ago by ★ 4.3k • written 5.6 years ago by ▴ 360
0
votes
5
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1.2k
views
[ChIPpeakAnno] Can not start ChIPpeakAnno after update to version 2.5.9
ChIPpeakAnno ChIPpeakAnno
updated 10.1 years ago by 13k • written 10.1 years ago by ▴ 90
0
votes
4
replies
762
views
ChIPpeakAnno
convert ChIPpeakAnno convert ChIPpeakAnno
9.8 years ago Julie Zhu ★ 4.3k
1
vote
4
replies
971
views
ChIPpeakAnno binOverGene error
chippeakanno binOverGene
updated 4.6 years ago by ★ 1.3k • written 4.6 years ago by • 0
5
votes
4
replies
2.9k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r ChIPpeakAnno
5.2 years ago • updated 4.9 years ago salamandra ▴ 20
0
votes
4
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937
views
about ChIPpeakAnno
Annotation ChIPpeakAnno Annotation ChIPpeakAnno
11.8 years ago Julie Zhu ★ 4.3k
0
votes
4
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838
views
question regarding ChIPPeakAnno use
ChIPpeakAnno ChIPpeakAnno
updated 10.3 years ago by ▴ 20 • written 10.3 years ago by ★ 4.3k
0
votes
4
replies
876
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more question about makeVennDiagram
GO ChIPpeakAnno GO ChIPpeakAnno
9.9 years ago Julie Zhu ★ 4.3k
0
votes
4
replies
741
views
Suggestion for a small change to ChIPpeakAnno
ChIPpeakAnno ChIPpeakAnno
8.0 years ago Julie Zhu ★ 4.3k
0
votes
4
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1.6k
views
ChIPpeakAnno as.data.frame error
GO AnnotationData annotate convert ChIPpeakAnno GO AnnotationData annotate convert
updated 10.3 years ago by ★ 4.3k • written 10.3 years ago by ▴ 910
0
votes
4
replies
683
views
Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
7 months ago Tongjun • 0
0
votes
4
replies
560
views
chippeakanno file reading error
ChiPpeakAnno
3.2 years ago saddamhusain77 • 0
2
votes
4
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968
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ChIPpeakAnno annotatePeakInBatch output
chippeakanno
6.4 years ago igor ▴ 40
0
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3
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625
views
ChipPeakAnno - slightly different results between makeVennDiagram and findPeakOverlaps
Genetics ChIPpeakAnno Genetics ChIPpeakAnno
updated 9.7 years ago by ★ 1.3k • written 9.7 years ago by ▴ 480
0
votes
3
replies
744
views
ChIPpeakAnno
Transcription ChIPpeakAnno Transcription ChIPpeakAnno
12.4 years ago • updated 12.3 years ago Julie Zhu ★ 4.3k
4
votes
3
replies
787
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 5.0 years ago by ★ 1.3k • written 5.0 years ago by ▴ 110
0
votes
3
replies
801
views
strange ChIPpeakAnno and rtracklayer interaction.
GO annotate rtracklayer ChIPpeakAnno GO annotate rtracklayer ChIPpeakAnno
updated 11.7 years ago by 11k • written 11.7 years ago by ▴ 20
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3
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1.4k
views
ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is different than output of ol1$overlappingPeaks
chippeakanno
updated 5.2 years ago by ★ 1.3k • written 5.2 years ago by • 0
0
votes
3
replies
739
views
RE ChIPPEAKANNO
miRNA Genetics ChIPpeakAnno miRNA Genetics ChIPpeakAnno
9.8 years ago Julie Zhu ★ 4.3k
0
votes
3
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1.2k
views
ChIPpeakAnno to find peaks nearest to miRNA
miRNA GO BSgenome BSgenome ChIPpeakAnno miRNA GO BSgenome BSgenome ChIPpeakAnno
updated 9.9 years ago by ★ 4.3k • written 9.9 years ago by ▴ 350
0
votes
3
replies
992
views
ChIPpeakAnno problem w getAllPeakSequence()
GO annotate ChIPpeakAnno GO annotate ChIPpeakAnno
updated 9.7 years ago by ★ 1.3k • written 9.7 years ago by ▴ 50
0
votes
3
replies
744
views
integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno assignChromosomeRegion
updated 4.4 years ago by ★ 4.3k • written 4.4 years ago by ▴ 740
0
votes
3
replies
675
views
ChIPpeakAnno 2.12.2 bug
ChIPpeakAnno ChIPpeakAnno
updated 7.9 years ago by ★ 1.3k • written 7.9 years ago by ★ 4.3k
0
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3
replies
1.0k
views
CHiPpeakAnno GO and/or KEGG results presenting
chippeakanno go kegg graphics
6.2 years ago lokapal • 0
0
votes
3
replies
1.5k
views
ChIPpeakAnno: TSS at - strand
Annotation convert ChIPpeakAnno Annotation convert ChIPpeakAnno
8.4 years ago Julie Zhu ★ 4.3k
0
votes
3
replies
1.0k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
8.9 years ago Alan Smith ▴ 150
0
votes
3
replies
858
views
chippeakanno:::addGeneID for adding gene symbol etc. to annotatedPeak or enrichedGO
Annotation convert biomaRt bridge ChIPpeakAnno Annotation convert biomaRt bridge
updated 10.9 years ago by ▴ 810 • written 10.9 years ago by ★ 4.3k
0
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3
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generate RangedData from DiffBind
chippeakanno diffbind
7.6 years ago joydeepbhadury • 0
50 results • Page 1 of 1
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Answer: miRNA differential expression analysis - treat as transcript level? by Michael Love 37k
If it's "ok" depends on the amount of inferential uncertainty. We have benchmarked typical gene-level methods and found that we don't gain …
Comment: RSEM - tximport; where is effective_length information used? Implications for sc by Michael Love 37k
@atpoint is correct -- it's not enough to say single-cell. In the tximport vignette we have a note about transcript length correction for 3…
Comment: Help with limma contrast, difference of a difference? by Ahdee ▴ 50
thanks yes, I think this is useful and looks very nice as well. I color coded up significant up or down nc==no significant change based on …
Comment: Help with limma contrast, difference of a difference? by Ahdee ▴ 50
all this time I did not thought to use this. VennDiagram was super useful but the the table even more useful to do some fast comparisons. …
Comment: Help with limma contrast, difference of a difference? by Steve Lianoglou 13k
great, let us know how it goes!
Votes
Answer: Help with limma contrast, difference of a difference?
Answer: Help with limma contrast, difference of a difference?
Answer: Help with limma contrast, difference of a difference?
Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin
Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin
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