Showing : Chippeakanno • reset
0
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3
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442
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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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470
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
7 months ago Raghad • 0
0
votes
0
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499
views
Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
10 months ago nilanjanamani88 • 0
1
vote
5
replies
1.1k
views
ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
14 months ago ilaria.maurizio • 0
0
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0
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494
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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
votes
7
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1.4k
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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
votes
1
reply
732
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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921
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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
votes
16
replies
2.3k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
21 months ago • updated 20 months ago Chris ▴ 20
1
vote
2
replies
875
views
How to map geneIds to ENTREZIDs
Xenopus_laevis ChIPpeakAnno
23 months ago stacy.genovese • 0
1
vote
1
reply
793
views
Interpretation of $vennCounts output "Others"
ChIPpeakAnno
updated 2.0 years ago by ★ 1.3k • written 2.0 years ago by ▴ 10
0
votes
2
replies
923
views
Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
2.2 years ago michela ▴ 20
0
votes
1
reply
772
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
vote
1
reply
848
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
2.4 years ago mehdi • 0
0
votes
1
reply
886
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
votes
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
961
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.1 years ago Nadav • 0
1
vote
2
replies
3.0k
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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2.5k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
3.2 years ago Tongjun • 0
1
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6
replies
1.9k
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
3.5 years ago Arunima ▴ 10
1
vote
3
replies
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 4.4 years ago by ▴ 140
2
votes
2
replies
1.0k
views
how to suppress makeVennDiagram plot
ChIPpeakAnno
4.4 years ago C T ▴ 140
1
vote
2
replies
1.1k
views
How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
ChIPpeakAnno
5.4 years ago liruiradiant • 0
0
votes
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
5.8 years ago saddamhusain77 • 0
1
vote
6
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1.6k
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
5.9 years ago ngs06 ▴ 20
2
votes
10
replies
3.8k
views
ChIPpeakAnno, MACS format annotation
bioconductor ChIPpeakAnno
updated 6.0 years ago by ★ 4.3k • written 7.8 years ago by ▴ 30
0
votes
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
6.5 years ago 94133 • 0
0
votes
1
reply
1.4k
views
Error creating pool for permutation test (PeakPermTest)
permutation pool chippeakanno
6.5 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 6.9 years ago by ★ 6.6k • written 6.9 years ago by ▴ 70
0
votes
3
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1.6k
views
integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno assignChromosomeRegion
updated 6.9 years ago by ★ 4.3k • written 6.9 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 12.1 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 8.3 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 7.5 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 7.7 years ago by 25k • written 7.7 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 7.8 years ago by ★ 1.3k • written 7.8 years ago by • 0
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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
It is not possible to use both. estimateGLMRobustDisp() estimates negative binomial dispersions for each gene, whereas glmQLFit() estimates…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0
Thank you. What is the difference between setting robust=TRUE in glmQLFit and estimateGLMRobustDisp? The paper i mentioned in the post used…
Comment: PCA of different bacterial species by Jeremy • 0
Your approach of using ~2500 single-copy orthologs and normalizing with VST or rlog for PCA is valid for exploring general clustering [pap…
Comment: RnBeads::combine() - error? by Urotree • 0
pheno <- rnb.set.arrays@pheno # Phenotypic data sites <- rnb.set.arrays@sites # CpG site definitions (data.frame) meth <- rnb.set…
Comment: RnBeads::combine() - error? by Urotree • 0
![enter image description here][1] [1]: /media/images/40d9778d-b044-4405-9b3d-2ba835f6 Hi, after I convert to RnBiseqSet, it shows "All…
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Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
scater/scran with TPMs from Salmon - counts?
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