Showing : chippeakanno • reset
0
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239
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ChIPpeakAnno can not load data
genomes ChIPpeakAnno
updated 7 weeks ago by ▴ 10 • written 7 weeks ago by • 0
0
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0
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348
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
5 months ago Raghad • 0
0
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0
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443
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
9 months ago nilanjanamani88 • 0
1
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5
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941
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ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
12 months ago ilaria.maurizio • 0
0
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0
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462
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
13 months ago franciscrick41 • 0
3
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7
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1.3k
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 14 months ago by ▴ 20
2
votes
14
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1.6k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 14 months ago by 67k • written 14 months ago by ▴ 10
0
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1
reply
672
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genomeStyles error in ChIPpeakAnno
Chippeakanno ChIPpeakAnno
updated 15 months ago by 67k • written 15 months ago by • 0
0
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2
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850
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 18 months ago by ▴ 70 • written 18 months ago by ▴ 140
9
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16
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2.2k
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How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
19 months ago • updated 18 months ago Chris ▴ 20
1
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2
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823
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How to map geneIds to ENTREZIDs
Xenopus_laevis ChIPpeakAnno
21 months ago stacy.genovese • 0
1
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1
reply
765
views
Interpretation of $vennCounts output "Others"
ChIPpeakAnno
updated 22 months ago by ★ 1.3k • written 22 months ago by ▴ 10
0
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2
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890
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Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
2.1 years ago michela ▴ 20
0
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1
reply
743
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Trying to understand the `select` option in `annotatePeakInBatch` function of `ChIPpeakAnno` package.
ChIPpeakAnno
updated 2.2 years ago by 67k • written 2.2 years ago by • 0
1
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1
reply
819
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How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
2.3 years ago mehdi • 0
0
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1
reply
850
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AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.5 years ago by ★ 1.3k • written 2.5 years ago by • 0
0
votes
1
reply
1.0k
views
peak annotation
ChIPpeakAnno Annotation
updated 2.6 years ago by ▴ 70 • written 2.7 years ago by ▴ 670
1
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2
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1.9k
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another problem when converting bed to granges using togranges
ChIPpeakAnno
2.7 years ago Bakhtiyar • 0
0
votes
2
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1.1k
views
ChIP-seq or CUT&RUN enrichment
ChIPQC ChIPpeakAnno
2.7 years ago Bogdan ▴ 670
2
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6
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2.7k
views
Problem converting a bed file to granges using togranges chippeakanno
ChIPpeakAnno
updated 2.8 years ago by ▴ 70 • written 2.8 years ago by • 0
0
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0
replies
929
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.9 years ago Nadav • 0
1
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2
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2.8k
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ChIPpeakAnno findOverlapsOfPeaks error: "Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs."
HELP ChIPpeakAnno
3.0 years ago lexi.kellington • 0
0
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4
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2.3k
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Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
3.0 years ago Tongjun • 0
1
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6
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1.8k
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
3.4 years ago Arunima ▴ 10
1
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3
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1.1k
views
genomicElementDistribution function not found
ChIPpeakAnno
updated 3.4 years ago by ★ 4.3k • written 3.4 years ago by ▴ 10
2
votes
2
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1.5k
views
Hello how to use ChIPpeakAnno for latest version of ensemble genome aligned data
ChIPpeakAnno
3.7 years ago Lucky • 0
7
votes
9
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2.3k
views
counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 4.2 years ago by ★ 4.3k • written 4.2 years ago by ▴ 140
2
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2
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962
views
how to suppress makeVennDiagram plot
ChIPpeakAnno
4.3 years ago C T ▴ 140
1
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2
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1.1k
views
How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
ChIPpeakAnno
5.3 years ago liruiradiant • 0
0
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1
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1.3k
views
Unable to annotate in ChIPQC using yeast genome
ChIPQC GenomicRanges ChIPpeakAnno
updated 3.5 years ago by • 0 • written 5.5 years ago by • 0
0
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4
replies
1.4k
views
chippeakanno file reading error
ChiPpeakAnno
5.6 years ago saddamhusain77 • 0
1
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6
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1.6k
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
5.7 years ago ngs06 ▴ 20
2
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10
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3.7k
views
ChIPpeakAnno, MACS format annotation
bioconductor ChIPpeakAnno
updated 5.8 years ago by ★ 4.3k • written 7.6 years ago by ▴ 30
0
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7
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1.8k
views
ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 6.1 years ago by ★ 1.3k • written 6.1 years ago by • 0
3
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6
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1.8k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
6.3 years ago 94133 • 0
0
votes
1
reply
1.3k
views
Error creating pool for permutation test (PeakPermTest)
permutation pool chippeakanno
6.3 years ago ge2sasag • 0
1
vote
1
reply
1.1k
views
Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap chippeakanno
updated 6.5 years ago by ★ 1.3k • written 6.5 years ago by • 0
2
votes
2
replies
1.8k
views
Can't install ChIPpeakanno - "libmysqlclient was not found" - do I need to remove latest version of R?
ChIPpeakAnno
updated 6.7 years ago by ★ 6.6k • written 6.7 years ago by ▴ 70
0
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3
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1.6k
views
integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno assignChromosomeRegion
updated 6.7 years ago by ★ 4.3k • written 6.7 years ago by ▴ 740
1
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1
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1.1k
views
Custom regions in assignChromosomeRegion?
chippeakanno
updated 6.8 years ago by ★ 1.3k • written 6.8 years ago by • 0
1
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2
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2.7k
views
Error : object path is not exported by namespace:Rsamtools
packages installation problem rsamtools chippeakanno ensembldb
6.9 years ago inzirio ▴ 10
1
vote
4
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1.7k
views
ChIPpeakAnno binOverGene error
chippeakanno binOverGene
updated 6.9 years ago by ★ 1.3k • written 7.0 years ago by • 0
0
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1
reply
1.3k
views
ChIPpeakAnno to find peaks nearest to miRNA
ChIPpeakAnno ChIPpeakAnno
updated 7.0 years ago by • 0 • written 11.9 years ago by ▴ 120
2
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3
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2.9k
views
org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
chippeakanno annotationdbi
updated 7.0 years ago by • 0 • written 9.0 years ago by • 0
0
votes
1
reply
1.5k
views
featureAlignedSignal() error: deparse(sig): object 'sig' not found.
bioconductor chippeakanno featureAlignedDistribution featureAlignedSignal
updated 7.0 years ago by • 0 • written 8.1 years ago by • 0
0
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1
reply
1.1k
views
Help for ChIP script !! Error message while installing packages
annotation chippeakanno
updated 7.1 years ago by 25k • written 7.1 years ago by • 0
5
votes
4
replies
5.2k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r ChIPpeakAnno
7.6 years ago • updated 7.3 years ago salamandra ▴ 20
4
votes
3
replies
1.5k
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 7.4 years ago by ★ 1.3k • written 7.4 years ago by ▴ 110
1
vote
1
reply
1.3k
views
Regarding ChIPpeakAnno installation error
chippeakanno
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 10
0
votes
3
replies
2.8k
views
ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is different than output of ol1$overlappingPeaks
chippeakanno
updated 7.6 years ago by ★ 1.3k • written 7.6 years ago by • 0
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Comment: How many of my genes from my gene list are in each KEGG pathway? by josephasmith1310 • 0
> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…
Comment: EuroBioC2024 abstract submission is open! by Esperan • 0
Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Comment: Adjusted p-values become NA when sub-setting samples by txema.heredia • 0
Thanks! I've been looking into DESeq2's code and, indeed, I get matching results when running manually the code inherited from the `genefi…
Answer: DESeq2 interaction between cancer cells and microenvironment cells by Michael Love 42k
I don't really know what you mean by "come from the contamination". You can look at the main effects and the interaction, but I don't know …
Votes
Answer: How do I merge a list of GRanges?
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
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