Showing : Chippeakanno • reset
0
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3
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431
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ChIPpeakAnno can not load data
genomes ChIPpeakAnno
written 3 months ago by • 0
0
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0
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445
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
7 months ago Raghad • 0
0
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0
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489
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
10 months ago nilanjanamani88 • 0
1
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5
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1.0k
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ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
14 months ago ilaria.maurizio • 0
0
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0
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485
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
15 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 15 months ago by ▴ 20
2
votes
14
replies
1.7k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 16 months ago by 67k • written 16 months ago by ▴ 10
0
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1
reply
724
views
genomeStyles error in ChIPpeakAnno
Chippeakanno ChIPpeakAnno
updated 17 months ago by 67k • written 17 months ago by • 0
0
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2
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904
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 20 months ago by ▴ 70 • written 20 months ago by ▴ 140
9
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16
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2.3k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
20 months ago Chris ▴ 20
1
vote
2
replies
862
views
How to map geneIds to ENTREZIDs
Xenopus_laevis ChIPpeakAnno
22 months ago stacy.genovese • 0
1
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1
reply
784
views
Interpretation of $vennCounts output "Others"
ChIPpeakAnno
updated 24 months ago by ★ 1.3k • written 24 months ago by ▴ 10
0
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2
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913
views
Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
2.2 years ago michela ▴ 20
0
votes
1
reply
765
views
Trying to understand the `select` option in `annotatePeakInBatch` function of `ChIPpeakAnno` package.
ChIPpeakAnno
updated 2.3 years ago by 67k • written 2.3 years ago by • 0
1
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1
reply
843
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
2.4 years ago mehdi • 0
0
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1
reply
878
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.6 years ago by ★ 1.3k • written 2.6 years ago by • 0
0
votes
1
reply
1.1k
views
peak annotation
ChIPpeakAnno Annotation
updated 2.7 years ago by ▴ 70 • written 2.8 years ago by ▴ 670
1
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2
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2.0k
views
another problem when converting bed to granges using togranges
ChIPpeakAnno
2.9 years ago Bakhtiyar • 0
0
votes
2
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1.1k
views
ChIP-seq or CUT&RUN enrichment
ChIPQC ChIPpeakAnno
2.9 years ago Bogdan ▴ 670
2
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6
replies
2.9k
views
Problem converting a bed file to granges using togranges chippeakanno
ChIPpeakAnno
updated 2.9 years ago by ▴ 70 • written 2.9 years ago by • 0
0
votes
0
replies
952
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.0 years ago Nadav • 0
1
vote
2
replies
2.9k
views
ChIPpeakAnno findOverlapsOfPeaks error: "Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs."
HELP ChIPpeakAnno
3.1 years ago lexi.kellington • 0
0
votes
4
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2.4k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
3.1 years ago Tongjun • 0
1
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6
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1.9k
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
3.5 years ago Arunima ▴ 10
1
vote
3
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1.1k
views
genomicElementDistribution function not found
ChIPpeakAnno
updated 3.5 years ago by ★ 4.3k • written 3.5 years ago by ▴ 10
2
votes
2
replies
1.6k
views
Hello how to use ChIPpeakAnno for latest version of ensemble genome aligned data
ChIPpeakAnno
3.8 years ago Lucky • 0
7
votes
9
replies
2.4k
views
counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 4.3 years ago by ★ 4.3k • written 4.3 years ago by ▴ 140
2
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2
replies
1.0k
views
how to suppress makeVennDiagram plot
ChIPpeakAnno
4.4 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
5.4 years ago liruiradiant • 0
0
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1
reply
1.3k
views
Unable to annotate in ChIPQC using yeast genome
ChIPQC GenomicRanges ChIPpeakAnno
updated 3.6 years ago by • 0 • written 5.6 years ago by • 0
0
votes
4
replies
1.5k
views
chippeakanno file reading error
ChiPpeakAnno
5.7 years ago saddamhusain77 • 0
1
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6
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1.6k
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
5.8 years ago ngs06 ▴ 20
2
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10
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3.7k
views
ChIPpeakAnno, MACS format annotation
bioconductor ChIPpeakAnno
updated 5.9 years ago by ★ 4.3k • written 7.7 years ago by ▴ 30
0
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7
replies
1.8k
views
ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 6.3 years ago by ★ 1.3k • written 6.3 years ago by • 0
3
votes
6
replies
1.9k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
6.4 years ago 94133 • 0
0
votes
1
reply
1.3k
views
Error creating pool for permutation test (PeakPermTest)
permutation pool chippeakanno
6.4 years ago ge2sasag • 0
1
vote
1
reply
1.1k
views
Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap chippeakanno
updated 6.7 years ago by ★ 1.3k • written 6.7 years ago by • 0
2
votes
2
replies
1.9k
views
Can't install ChIPpeakanno - "libmysqlclient was not found" - do I need to remove latest version of R?
ChIPpeakAnno
updated 6.8 years ago by ★ 6.6k • written 6.8 years ago by ▴ 70
0
votes
3
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1.6k
views
integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno assignChromosomeRegion
updated 6.8 years ago by ★ 4.3k • written 6.8 years ago by ▴ 740
1
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1
reply
1.1k
views
Custom regions in assignChromosomeRegion?
chippeakanno
updated 6.9 years ago by ★ 1.3k • written 6.9 years ago by • 0
1
vote
2
replies
2.7k
views
Error : object path is not exported by namespace:Rsamtools
packages installation problem rsamtools chippeakanno ensembldb
7.0 years ago inzirio ▴ 10
1
vote
4
replies
1.7k
views
ChIPpeakAnno binOverGene error
chippeakanno binOverGene
updated 7.1 years ago by ★ 1.3k • written 7.1 years ago by • 0
0
votes
1
reply
1.3k
views
ChIPpeakAnno to find peaks nearest to miRNA
ChIPpeakAnno ChIPpeakAnno
updated 7.2 years ago by • 0 • written 12.0 years ago by ▴ 120
2
votes
3
replies
3.0k
views
org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
chippeakanno annotationdbi
updated 7.2 years ago by • 0 • written 9.2 years ago by • 0
0
votes
1
reply
1.6k
views
featureAlignedSignal() error: deparse(sig): object 'sig' not found.
bioconductor chippeakanno featureAlignedDistribution featureAlignedSignal
updated 7.2 years ago by • 0 • written 8.2 years ago by • 0
0
votes
1
reply
1.1k
views
Help for ChIP script !! Error message while installing packages
annotation chippeakanno
updated 7.2 years ago by 25k • written 7.2 years ago by • 0
5
votes
4
replies
5.3k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r ChIPpeakAnno
7.7 years ago • updated 7.4 years ago salamandra ▴ 20
4
votes
3
replies
1.5k
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 7.5 years ago by ★ 1.3k • written 7.5 years ago by ▴ 110
1
vote
1
reply
1.3k
views
Regarding ChIPpeakAnno installation error
chippeakanno
updated 7.6 years ago by 25k • written 7.6 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 7.7 years ago by ★ 1.3k • written 7.7 years ago by • 0
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Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Hervé Pagès 16k
> I have requested gDNAx developers for a feature request to turn off seqlevelsStyle(txdb) Yes, that's the right course of action. `seqlev…
Comment: ISO a solution to rank-order introns by transcript by mat149 ▴ 80
Hey, In revisiting this question, the following code works for the '+' strand. I am having issues with demarcating intron rank by transcri…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…
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C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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