Showing : ChiPpeakAnno • reset
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153
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
11 weeks ago nilanjanamani88 • 0
1
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5
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548
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ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
6 months ago ilaria.maurizio • 0
0
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0
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276
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
7 months ago franciscrick41 • 0
3
votes
7
replies
846
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
2
votes
14
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1.1k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 8 months ago by 65k • written 8 months ago by ▴ 10
0
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1
reply
477
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genomeStyles error in ChIPpeakAnno
Chippeakanno ChIPpeakAnno
updated 9 months ago by 65k • written 9 months ago by • 0
0
votes
2
replies
594
views
annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 12 months ago by ▴ 70 • written 12 months ago by ▴ 140
9
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16
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1.7k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
12 months ago Chris • 0
1
vote
2
replies
625
views
How to map geneIds to ENTREZIDs
Xenopus_laevis ChIPpeakAnno
15 months ago stacy.genovese • 0
1
vote
1
reply
599
views
Interpretation of $vennCounts output "Others"
ChIPpeakAnno
updated 16 months ago by ★ 1.3k • written 16 months ago by ▴ 10
0
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2
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713
views
Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
18 months ago michela ▴ 20
0
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1
reply
580
views
Trying to understand the `select` option in `annotatePeakInBatch` function of `ChIPpeakAnno` package.
ChIPpeakAnno
updated 20 months ago by 65k • written 20 months ago by • 0
1
vote
1
reply
625
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
20 months ago mehdi • 0
0
votes
1
reply
702
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 23 months ago by ★ 1.3k • written 23 months ago by • 0
0
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1
reply
789
views
peak annotation
ChIPpeakAnno Annotation
updated 2.0 years ago by ▴ 70 • written 2.1 years ago by ▴ 670
1
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2
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1.7k
views
another problem when converting bed to granges using togranges
ChIPpeakAnno
2.2 years ago Bakhtiyar • 0
0
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2
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888
views
ChIP-seq or CUT&RUN enrichment
ChIPQC ChIPpeakAnno
2.2 years ago Bogdan ▴ 670
2
votes
6
replies
2.1k
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
0
votes
0
replies
736
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.4 years ago Nadav • 0
1
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2
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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
0
votes
4
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2.1k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
2.5 years ago Tongjun • 0
1
vote
6
replies
1.5k
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
2.8 years ago Arunima ▴ 10
1
vote
3
replies
907
views
genomicElementDistribution function not found
ChIPpeakAnno
updated 2.8 years ago by ★ 4.3k • written 2.8 years ago by ▴ 10
2
votes
2
replies
1.3k
views
Hello how to use ChIPpeakAnno for latest version of ensemble genome aligned data
ChIPpeakAnno
3.1 years ago Lucky • 0
7
votes
9
replies
1.8k
views
counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 3.6 years ago by ★ 4.3k • written 3.7 years ago by ▴ 140
2
votes
2
replies
797
views
how to suppress makeVennDiagram plot
ChIPpeakAnno
3.7 years ago C T ▴ 140
1
vote
2
replies
951
views
How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
ChIPpeakAnno
4.7 years ago liruiradiant • 0
0
votes
1
reply
1.1k
views
Unable to annotate in ChIPQC using yeast genome
ChIPQC GenomicRanges ChIPpeakAnno
updated 3.0 years ago by • 0 • written 5.0 years ago by • 0
0
votes
4
replies
1.2k
views
chippeakanno file reading error
ChiPpeakAnno
5.1 years ago saddamhusain77 • 0
1
vote
6
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1.3k
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
5.2 years ago ngs06 ▴ 20
0
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7
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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
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
0
votes
1
reply
1.1k
views
Error creating pool for permutation test (PeakPermTest)
permutation pool chippeakanno
5.8 years ago ge2sasag • 0
1
vote
1
reply
957
views
Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap chippeakanno
updated 6.0 years ago by ★ 1.3k • written 6.0 years ago by • 0
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
0
votes
3
replies
1.3k
views
integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno assignChromosomeRegion
updated 6.2 years ago by ★ 4.3k • written 6.2 years ago by ▴ 740
1
vote
1
reply
935
views
Custom regions in assignChromosomeRegion?
chippeakanno
updated 6.2 years ago by ★ 1.3k • written 6.2 years ago by • 0
1
vote
2
replies
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 6.4 years ago by • 0
0
votes
1
reply
949
views
Help for ChIP script !! Error message while installing packages
annotation chippeakanno
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
4
votes
3
replies
1.3k
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 6.8 years ago by ★ 1.3k • written 6.8 years ago by ▴ 110
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
5
votes
4
replies
4.7k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r ChIPpeakAnno
7.0 years ago • updated 6.8 years ago salamandra ▴ 20
0
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3
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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
2
votes
10
replies
3.2k
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 7.1 years ago by ▴ 80
2
votes
3
replies
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
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
3
votes
5
replies
3.5k
views
Error with ChIPpeakAnno Ensembl annotation
ChIPpeakAnno genomicfeatures
updated 7.4 years ago by ★ 4.3k • written 7.4 years ago by ▴ 360
0
votes
1
reply
1.3k
views
featureAlignedSignal() error: deparse(sig): object 'sig' not found.
bioconductor chippeakanno featureAlignedDistribution featureAlignedSignal
updated 6.5 years ago by • 0 • written 7.6 years ago by • 0
50 results • Page 1 of 1
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Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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