Showing : chippeakanno • reset
9
votes
16
replies
1.7k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
12 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 7.9 years ago by ★ 4.3k • written 7.9 years ago by ▴ 140
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
4
votes
12
replies
2.6k
views
Curious behaviour of ChIPpeakAnno
chippeakanno
updated 9.5 years ago by ★ 1.3k • written 9.5 years ago by ▴ 20
0
votes
12
replies
2.4k
views
more stupid *Ranges questions...
Transcription ChIPpeakAnno GenomicRanges Transcription ChIPpeakAnno GenomicRanges
updated 12.6 years ago by ★ 11k • written 12.6 years ago by ★ 4.2k
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
22
votes
10
replies
7.4k
views
Error in GRanges: could not find symbol "recursive" in environment of the generic function
granges chippeakanno
updated 7.1 years ago by ▴ 10 • written 7.2 years ago by ▴ 80
1
vote
9
replies
3.7k
views
ChIPpeakAnno: findOverlapsOfPeaks keep GRanges metadata
chippeakanno findOverlapsOfPeaks
updated 8.9 years ago by ▴ 240 • written 9.0 years ago by ▴ 30
7
votes
9
replies
1.9k
views
counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 3.7 years ago by ★ 4.3k • written 3.7 years ago by ▴ 140
0
votes
8
replies
1.6k
views
ChIPpeakAnno Strandedness and distance calculation
Annotation Cancer ChIPpeakAnno Annotation Cancer ChIPpeakAnno
updated 14.0 years ago by ★ 1.5k • written 14.0 years ago by ★ 4.3k
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
3
votes
7
replies
861
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months 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
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
7
replies
1.5k
views
ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 5.6 years ago by ★ 1.3k • written 5.6 years ago by • 0
0
votes
7
replies
1.4k
views
Problem loading BED file with BED2RangedData
GO ChIPpeakAnno GO ChIPpeakAnno
updated 11.4 years ago by ★ 1.3k • written 11.4 years ago by ▴ 280
2
votes
6
replies
2.2k
views
Problem converting a bed file to granges using togranges chippeakanno
ChIPpeakAnno
updated 2.2 years ago by ▴ 70 • written 2.2 years ago by • 0
3
votes
6
replies
1.6k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
5.8 years ago 94133 • 0
1
vote
6
replies
1.5k
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
2.9 years ago • updated 2.8 years ago Arunima ▴ 10
0
votes
6
replies
1.6k
views
Question RE: getEnrichedGo in ChIPpeakAnno package
Yeast ChIPpeakAnno Starr Yeast ChIPpeakAnno Starr
updated 13.9 years ago by ★ 4.3k • written 13.9 years ago by ▴ 410
1
vote
6
replies
1.4k
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
5.2 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 ★ 1.3k • written 9.3 years ago by ▴ 20
3
votes
5
replies
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
0
votes
5
replies
1.1k
views
ChIPpeakAnno question--peak aggregation over bins from TSS
ChIPpeakAnno ChIPpeakAnno
updated 11.3 years ago by ★ 4.3k • written 11.3 years ago by ▴ 40
0
votes
5
replies
1.4k
views
Query on ChipPeakAnno: AnnotatePeakinBatch input
Annotation Cancer ChIPpeakAnno Annotation Cancer ChIPpeakAnno
updated 10.4 years ago by ▴ 30 • written 10.4 years ago by ★ 4.3k
4
votes
5
replies
1.7k
views
ChIPpeakAnno getAnnotation request fail
chippeakanno biomart ensembl
8.3 years ago igor ▴ 40
1
vote
5
replies
570
views
ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
6 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 11.9 years ago by ★ 13k • written 11.9 years ago by ▴ 90
0
votes
4
replies
1.2k
views
ChIPpeakAnno
convert ChIPpeakAnno convert ChIPpeakAnno
11.7 years ago Julie Zhu ★ 4.3k
1
vote
4
replies
1.5k
views
ChIPpeakAnno binOverGene error
chippeakanno binOverGene
updated 6.4 years ago by ★ 1.3k • written 6.4 years ago by • 0
5
votes
4
replies
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
0
votes
4
replies
1.2k
views
more question about makeVennDiagram
GO ChIPpeakAnno GO ChIPpeakAnno
11.8 years ago Julie Zhu ★ 4.3k
0
votes
4
replies
1.3k
views
about ChIPpeakAnno
Annotation ChIPpeakAnno Annotation ChIPpeakAnno
13.6 years ago Julie Zhu ★ 4.3k
0
votes
4
replies
1.3k
views
question regarding ChIPPeakAnno use
ChIPpeakAnno ChIPpeakAnno
updated 12.1 years ago by ▴ 20 • written 12.1 years ago by ★ 4.3k
0
votes
4
replies
1.1k
views
Suggestion for a small change to ChIPpeakAnno
ChIPpeakAnno ChIPpeakAnno
9.8 years ago Julie Zhu ★ 4.3k
0
votes
4
replies
2.2k
views
ChIPpeakAnno as.data.frame error
GO AnnotationData annotate convert ChIPpeakAnno GO AnnotationData annotate convert
updated 12.2 years ago by ★ 4.3k • written 12.2 years ago by ▴ 910
0
votes
4
replies
2.1k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
2.5 years ago Tongjun • 0
0
votes
4
replies
1.2k
views
chippeakanno file reading error
ChiPpeakAnno
5.1 years ago saddamhusain77 • 0
2
votes
4
replies
1.7k
views
ChIPpeakAnno annotatePeakInBatch output
chippeakanno
8.3 years ago igor ▴ 40
0
votes
3
replies
1.1k
views
ChipPeakAnno - slightly different results between makeVennDiagram and findPeakOverlaps
Genetics ChIPpeakAnno Genetics ChIPpeakAnno
updated 11.6 years ago by ★ 1.3k • written 11.6 years ago by ▴ 510
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
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
0
votes
3
replies
1.2k
views
strange ChIPpeakAnno and rtracklayer interaction.
GO annotate rtracklayer ChIPpeakAnno GO annotate rtracklayer ChIPpeakAnno
updated 13.5 years ago by ★ 11k • written 13.5 years ago by ▴ 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 7.1 years ago by ★ 1.3k • written 7.1 years ago by • 0
0
votes
3
replies
1.2k
views
RE ChIPPEAKANNO
miRNA Genetics ChIPpeakAnno miRNA Genetics ChIPpeakAnno
11.7 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 11.8 years ago by ★ 4.3k • written 11.8 years ago by ▴ 350
0
votes
3
replies
1.4k
views
ChIPpeakAnno problem w getAllPeakSequence()
GO annotate ChIPpeakAnno GO annotate ChIPpeakAnno
updated 11.6 years ago by ★ 1.3k • written 11.6 years ago by ▴ 50
0
votes
3
replies
1.4k
views
integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno assignChromosomeRegion
updated 6.2 years ago by ★ 4.3k • written 6.2 years ago by ▴ 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 12.7 years ago by ▴ 810 • written 12.8 years ago by ★ 4.3k
0
votes
3
replies
966
views
ChIPpeakAnno 2.12.2 bug
ChIPpeakAnno ChIPpeakAnno
updated 9.7 years ago by ★ 1.3k • written 9.7 years ago by ★ 4.3k
50 results • Page 1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to Zainab • 0
Popular Question to Theo ▴ 10
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Locations • All
The city by the bay, 6 minutes ago
WEHI, Melbourne, Australia, 17 minutes ago
France, 32 minutes ago
Iran, 43 minutes ago
San Diego, 1 hour ago
Traffic: 492 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6