Showing : Chippeakanno • reset
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3
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853
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ChIPpeakAnno can not load data
genomes ChIPpeakAnno
written 13 months ago by • 0
0
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0
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926
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
17 months ago Raghad • 0
0
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0
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787
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
21 months ago nilanjanamani88 • 0
1
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5
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1.7k
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ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
2.0 years ago ilaria.maurizio • 0
0
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0
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749
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
2.1 years ago franciscrick41 • 0
3
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7
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1.7k
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 2.1 years ago by ▴ 20
2
votes
14
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2.5k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 2.2 years ago by 68k • written 2.2 years ago by ▴ 10
0
votes
1
reply
913
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genomeStyles error in ChIPpeakAnno
Chippeakanno ChIPpeakAnno
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
votes
2
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1.3k
views
annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 2.5 years ago by ▴ 70 • written 2.5 years ago by ▴ 140
9
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16
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3.0k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
2.6 years ago • updated 2.5 years ago Chris ▴ 20
1
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2
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1.1k
views
How to map geneIds to ENTREZIDs
Xenopus_laevis ChIPpeakAnno
2.8 years ago stacy.genovese • 0
1
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1
reply
1.0k
views
Interpretation of $vennCounts output "Others"
ChIPpeakAnno
updated 2.9 years ago by ★ 1.3k • written 2.9 years ago by ▴ 10
0
votes
2
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1.2k
views
Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
3.0 years ago michela ▴ 20
0
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1
reply
1000
views
Trying to understand the `select` option in `annotatePeakInBatch` function of `ChIPpeakAnno` package.
ChIPpeakAnno
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
1
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1
reply
1.1k
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
3.2 years ago mehdi • 0
0
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1
reply
1.1k
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 3.5 years ago by ★ 1.3k • written 3.5 years ago by • 0
0
votes
1
reply
1.3k
views
peak annotation
ChIPpeakAnno Annotation
updated 3.5 years ago by ▴ 70 • written 3.6 years ago by ▴ 670
1
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2
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2.3k
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another problem when converting bed to granges using togranges
ChIPpeakAnno
3.7 years ago Bakhtiyar • 0
0
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2
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1.5k
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ChIP-seq or CUT&RUN enrichment
ChIPQC ChIPpeakAnno
3.7 years ago Bogdan ▴ 670
2
votes
6
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3.7k
views
Problem converting a bed file to granges using togranges chippeakanno
ChIPpeakAnno
updated 3.7 years ago by ▴ 70 • written 3.7 years ago by • 0
0
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0
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1.2k
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.9 years ago Nadav • 0
1
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2
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3.5k
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ChIPpeakAnno findOverlapsOfPeaks error: "Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs."
HELP ChIPpeakAnno
4.0 years ago lexi.kellington • 0
0
votes
4
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2.8k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
4.0 years ago Tongjun • 0
1
vote
6
replies
2.3k
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
4.4 years ago • updated 4.3 years ago Arunima ▴ 10
1
vote
3
replies
1.3k
views
genomicElementDistribution function not found
ChIPpeakAnno
updated 4.4 years ago by ★ 4.3k • written 4.4 years ago by ▴ 10
2
votes
2
replies
1.8k
views
Hello how to use ChIPpeakAnno for latest version of ensemble genome aligned data
ChIPpeakAnno
4.7 years ago Lucky • 0
7
votes
9
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3.0k
views
counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 5.2 years ago by ★ 4.3k • written 5.2 years ago by ▴ 140
2
votes
2
replies
1.2k
views
how to suppress makeVennDiagram plot
ChIPpeakAnno
5.2 years ago C T ▴ 140
1
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2
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1.3k
views
How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
ChIPpeakAnno
6.3 years ago liruiradiant • 0
0
votes
1
reply
1.5k
views
Unable to annotate in ChIPQC using yeast genome
ChIPQC GenomicRanges ChIPpeakAnno
updated 4.5 years ago by • 0 • written 6.5 years ago by • 0
0
votes
4
replies
1.8k
views
chippeakanno file reading error
ChiPpeakAnno
6.6 years ago saddamhusain77 • 0
1
vote
6
replies
1.9k
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
6.7 years ago ngs06 ▴ 20
2
votes
10
replies
4.3k
views
ChIPpeakAnno, MACS format annotation
bioconductor ChIPpeakAnno
updated 6.8 years ago by ★ 4.3k • written 8.6 years ago by ▴ 30
0
votes
7
replies
2.2k
views
ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 7.1 years ago by ★ 1.3k • written 7.1 years ago by • 0
3
votes
6
replies
2.2k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
7.3 years ago 94133 • 0
0
votes
1
reply
1.5k
views
Error creating pool for permutation test (PeakPermTest)
permutation pool chippeakanno
7.3 years ago ge2sasag • 0
1
vote
1
reply
1.3k
views
Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap chippeakanno
updated 7.5 years ago by ★ 1.3k • written 7.5 years ago by • 0
2
votes
2
replies
2.1k
views
Can't install ChIPpeakanno - "libmysqlclient was not found" - do I need to remove latest version of R?
ChIPpeakAnno
updated 7.7 years ago by ★ 6.6k • written 7.7 years ago by ▴ 70
0
votes
3
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1.8k
views
integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno assignChromosomeRegion
updated 7.7 years ago by ★ 4.3k • written 7.7 years ago by ▴ 740
1
vote
1
reply
1.3k
views
Custom regions in assignChromosomeRegion?
chippeakanno
updated 7.8 years ago by ★ 1.3k • written 7.8 years ago by • 0
1
vote
2
replies
3.0k
views
Error : object path is not exported by namespace:Rsamtools
packages installation problem rsamtools chippeakanno ensembldb
7.9 years ago inzirio ▴ 10
1
vote
4
replies
2.0k
views
ChIPpeakAnno binOverGene error
chippeakanno binOverGene
updated 7.9 years ago by ★ 1.3k • written 7.9 years ago by • 0
0
votes
1
reply
1.5k
views
ChIPpeakAnno to find peaks nearest to miRNA
ChIPpeakAnno ChIPpeakAnno
updated 8.0 years ago by • 0 • written 12.9 years ago by ▴ 120
2
votes
3
replies
3.3k
views
org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
chippeakanno annotationdbi
updated 8.0 years ago by • 0 • written 10.0 years ago by • 0
0
votes
1
reply
1.8k
views
featureAlignedSignal() error: deparse(sig): object 'sig' not found.
bioconductor chippeakanno featureAlignedDistribution featureAlignedSignal
updated 8.0 years ago by • 0 • written 9.1 years ago by • 0
0
votes
1
reply
1.3k
views
Help for ChIP script !! Error message while installing packages
annotation chippeakanno
updated 8.1 years ago by 25k • written 8.1 years ago by • 0
5
votes
4
replies
5.8k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r ChIPpeakAnno
8.6 years ago • updated 8.3 years ago salamandra ▴ 20
4
votes
3
replies
1.8k
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 8.4 years ago by ★ 1.3k • written 8.4 years ago by ▴ 110
1
vote
1
reply
1.5k
views
Regarding ChIPpeakAnno installation error
chippeakanno
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 10
0
votes
3
replies
3.2k
views
ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is different than output of ol1$overlappingPeaks
chippeakanno
updated 8.6 years ago by ★ 1.3k • written 8.6 years ago by • 0
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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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