Showing : chippeakanno • reset
0
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3
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528
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ChIPpeakAnno can not load data
genomes ChIPpeakAnno
written 5 months ago by • 0
0
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0
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593
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
9 months ago Raghad • 0
0
votes
0
replies
575
views
Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
12 months ago nilanjanamani88 • 0
1
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5
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1.2k
views
ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
16 months ago ilaria.maurizio • 0
0
votes
0
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547
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
17 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 17 months ago by ▴ 20
2
votes
14
replies
1.9k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 18 months ago by 68k • written 18 months ago by ▴ 10
0
votes
1
reply
787
views
genomeStyles error in ChIPpeakAnno
Chippeakanno ChIPpeakAnno
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
2
replies
993
views
annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 22 months ago by ▴ 70 • written 22 months ago by ▴ 140
9
votes
16
replies
2.4k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
23 months ago • updated 22 months ago Chris ▴ 20
1
vote
2
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933
views
How to map geneIds to ENTREZIDs
Xenopus_laevis ChIPpeakAnno
2.1 years ago stacy.genovese • 0
1
vote
1
reply
842
views
Interpretation of $vennCounts output "Others"
ChIPpeakAnno
updated 2.2 years ago by ★ 1.3k • written 2.2 years ago by ▴ 10
0
votes
2
replies
968
views
Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
2.4 years ago michela ▴ 20
0
votes
1
reply
826
views
Trying to understand the `select` option in `annotatePeakInBatch` function of `ChIPpeakAnno` package.
ChIPpeakAnno
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
1
vote
1
reply
909
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
2.6 years ago mehdi • 0
0
votes
1
reply
919
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.8 years ago by ★ 1.3k • written 2.8 years ago by • 0
0
votes
1
reply
1.1k
views
peak annotation
ChIPpeakAnno Annotation
updated 2.9 years ago by ▴ 70 • written 3.0 years ago by ▴ 670
1
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2
replies
2.1k
views
another problem when converting bed to granges using togranges
ChIPpeakAnno
3.1 years ago Bakhtiyar • 0
0
votes
2
replies
1.2k
views
ChIP-seq or CUT&RUN enrichment
ChIPQC ChIPpeakAnno
3.1 years ago Bogdan ▴ 670
2
votes
6
replies
3.1k
views
Problem converting a bed file to granges using togranges chippeakanno
ChIPpeakAnno
updated 3.1 years ago by ▴ 70 • written 3.1 years ago by • 0
0
votes
0
replies
1.0k
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.2 years ago Nadav • 0
1
vote
2
replies
3.1k
views
ChIPpeakAnno findOverlapsOfPeaks error: "Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs."
HELP ChIPpeakAnno
3.3 years ago lexi.kellington • 0
0
votes
4
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2.5k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
3.3 years ago Tongjun • 0
1
vote
6
replies
2.0k
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
3.7 years ago Arunima ▴ 10
1
vote
3
replies
1.1k
views
genomicElementDistribution function not found
ChIPpeakAnno
updated 3.7 years ago by ★ 4.3k • written 3.7 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
4.0 years ago Lucky • 0
7
votes
9
replies
2.6k
views
counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 4.5 years ago by ★ 4.3k • written 4.5 years ago by ▴ 140
2
votes
2
replies
1.1k
views
how to suppress makeVennDiagram plot
ChIPpeakAnno
4.6 years ago C T ▴ 140
1
vote
2
replies
1.2k
views
How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
ChIPpeakAnno
5.6 years ago liruiradiant • 0
0
votes
1
reply
1.3k
views
Unable to annotate in ChIPQC using yeast genome
ChIPQC GenomicRanges ChIPpeakAnno
updated 3.8 years ago by • 0 • written 5.8 years ago by • 0
0
votes
4
replies
1.6k
views
chippeakanno file reading error
ChiPpeakAnno
5.9 years ago saddamhusain77 • 0
1
vote
6
replies
1.7k
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
6.0 years ago ngs06 ▴ 20
2
votes
10
replies
3.9k
views
ChIPpeakAnno, MACS format annotation
bioconductor ChIPpeakAnno
updated 6.1 years ago by ★ 4.3k • written 7.9 years ago by ▴ 30
0
votes
7
replies
1.9k
views
ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 6.5 years ago by ★ 1.3k • written 6.5 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
6.6 years ago 94133 • 0
0
votes
1
reply
1.4k
views
Error creating pool for permutation test (PeakPermTest)
permutation pool chippeakanno
6.6 years ago ge2sasag • 0
1
vote
1
reply
1.2k
views
Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap chippeakanno
updated 6.9 years ago by ★ 1.3k • written 6.9 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 7.0 years ago by ★ 6.6k • written 7.0 years ago by ▴ 70
0
votes
3
replies
1.7k
views
integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno assignChromosomeRegion
updated 7.0 years ago by ★ 4.3k • written 7.0 years ago by ▴ 740
1
vote
1
reply
1.2k
views
Custom regions in assignChromosomeRegion?
chippeakanno
updated 7.1 years ago by ★ 1.3k • written 7.1 years ago by • 0
1
vote
2
replies
2.8k
views
Error : object path is not exported by namespace:Rsamtools
packages installation problem rsamtools chippeakanno ensembldb
7.2 years ago inzirio ▴ 10
1
vote
4
replies
1.8k
views
ChIPpeakAnno binOverGene error
chippeakanno binOverGene
updated 7.3 years ago by ★ 1.3k • written 7.3 years ago by • 0
0
votes
1
reply
1.4k
views
ChIPpeakAnno to find peaks nearest to miRNA
ChIPpeakAnno ChIPpeakAnno
updated 7.4 years ago by • 0 • written 12.2 years ago by ▴ 120
2
votes
3
replies
3.0k
views
org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
chippeakanno annotationdbi
updated 7.4 years ago by • 0 • written 9.4 years ago by • 0
0
votes
1
reply
1.6k
views
featureAlignedSignal() error: deparse(sig): object 'sig' not found.
bioconductor chippeakanno featureAlignedDistribution featureAlignedSignal
updated 7.4 years ago by • 0 • written 8.4 years ago by • 0
0
votes
1
reply
1.2k
views
Help for ChIP script !! Error message while installing packages
annotation chippeakanno
updated 7.4 years ago by 25k • written 7.4 years ago by • 0
5
votes
4
replies
5.5k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r ChIPpeakAnno
7.9 years ago • updated 7.6 years ago salamandra ▴ 20
4
votes
3
replies
1.6k
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 7.7 years ago by ★ 1.3k • written 7.7 years ago by ▴ 110
1
vote
1
reply
1.3k
views
Regarding ChIPpeakAnno installation error
chippeakanno
updated 7.8 years ago by 25k • written 7.8 years ago by ▴ 10
0
votes
3
replies
2.9k
views
ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is different than output of ol1$overlappingPeaks
chippeakanno
updated 7.9 years ago by ★ 1.3k • written 7.9 years ago by • 0
50 results • Page 1 of 1
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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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