Showing : chippeakanno • reset
0
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3
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470
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ChIPpeakAnno can not load data
genomes ChIPpeakAnno
written 4 months ago by • 0
0
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0
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534
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
8 months ago Raghad • 0
0
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0
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530
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
11 months ago nilanjanamani88 • 0
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5
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1.1k
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ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
15 months ago ilaria.maurizio • 0
0
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0
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517
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
16 months ago franciscrick41 • 0
3
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7
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1.4k
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 16 months ago by ▴ 20
2
votes
14
replies
1.8k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 17 months ago by 67k • written 17 months ago by ▴ 10
0
votes
1
reply
750
views
genomeStyles error in ChIPpeakAnno
Chippeakanno ChIPpeakAnno
updated 18 months ago by 67k • written 18 months ago by • 0
0
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2
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946
views
annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 21 months ago by ▴ 70 • written 21 months ago by ▴ 140
9
votes
16
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2.3k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
21 months ago Chris ▴ 20
1
vote
2
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896
views
How to map geneIds to ENTREZIDs
Xenopus_laevis ChIPpeakAnno
2.0 years ago stacy.genovese • 0
1
vote
1
reply
811
views
Interpretation of $vennCounts output "Others"
ChIPpeakAnno
updated 2.1 years ago by ★ 1.3k • written 2.1 years ago by ▴ 10
0
votes
2
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945
views
Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
2.3 years ago michela ▴ 20
0
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1
reply
790
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Trying to understand the `select` option in `annotatePeakInBatch` function of `ChIPpeakAnno` package.
ChIPpeakAnno
updated 2.4 years ago by 67k • written 2.4 years ago by • 0
1
vote
1
reply
874
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
2.5 years ago mehdi • 0
0
votes
1
reply
902
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.7 years ago by ★ 1.3k • written 2.7 years ago by • 0
0
votes
1
reply
1.1k
views
peak annotation
ChIPpeakAnno Annotation
updated 2.8 years ago by ▴ 70 • written 2.9 years ago by ▴ 670
1
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2
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2.1k
views
another problem when converting bed to granges using togranges
ChIPpeakAnno
3.0 years ago Bakhtiyar • 0
0
votes
2
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1.2k
views
ChIP-seq or CUT&RUN enrichment
ChIPQC ChIPpeakAnno
3.0 years ago Bogdan ▴ 670
2
votes
6
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3.0k
views
Problem converting a bed file to granges using togranges chippeakanno
ChIPpeakAnno
updated 3.0 years ago by ▴ 70 • written 3.0 years ago by • 0
0
votes
0
replies
980
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.2 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
3.2 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
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1.9k
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
3.6 years ago Arunima ▴ 10
1
vote
3
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1.1k
views
genomicElementDistribution function not found
ChIPpeakAnno
updated 3.6 years ago by ★ 4.3k • written 3.6 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
3.9 years ago Lucky • 0
7
votes
9
replies
2.5k
views
counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 4.4 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
4.5 years ago C T ▴ 140
1
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2
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1.2k
views
How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
ChIPpeakAnno
5.5 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 3.7 years ago by • 0 • written 5.7 years ago by • 0
0
votes
4
replies
1.5k
views
chippeakanno file reading error
ChiPpeakAnno
5.8 years ago saddamhusain77 • 0
1
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6
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1.7k
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
6.0 years ago ngs06 ▴ 20
2
votes
10
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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
1.9k
views
ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 6.4 years ago by ★ 1.3k • written 6.4 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 6.8 years ago by ★ 1.3k • written 6.8 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
1.6k
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
1.1k
views
Custom regions in assignChromosomeRegion?
chippeakanno
updated 7.0 years ago by ★ 1.3k • written 7.0 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
7.1 years ago inzirio ▴ 10
1
vote
4
replies
1.7k
views
ChIPpeakAnno binOverGene error
chippeakanno binOverGene
updated 7.2 years ago by ★ 1.3k • written 7.2 years ago by • 0
0
votes
1
reply
1.3k
views
ChIPpeakAnno to find peaks nearest to miRNA
ChIPpeakAnno ChIPpeakAnno
updated 7.3 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 7.3 years ago by • 0 • written 9.3 years ago by • 0
0
votes
1
reply
1.6k
views
featureAlignedSignal() error: deparse(sig): object 'sig' not found.
bioconductor chippeakanno featureAlignedDistribution featureAlignedSignal
updated 7.3 years ago by • 0 • written 8.4 years ago by • 0
0
votes
1
reply
1.1k
views
Help for ChIP script !! Error message while installing packages
annotation chippeakanno
updated 7.3 years ago by 25k • written 7.3 years ago by • 0
5
votes
4
replies
5.4k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r ChIPpeakAnno
7.8 years ago • updated 7.5 years ago salamandra ▴ 20
4
votes
3
replies
1.5k
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 7.6 years ago by ★ 1.3k • written 7.6 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
2.9k
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: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Comment: build samplesheet and plot profile by yf • 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
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Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
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