Showing : chippeakanno • reset
0
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3
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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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467
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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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496
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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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1.1k
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ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
14 months ago ilaria.maurizio • 0
0
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0
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493
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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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1.4k
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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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917
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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
20 months ago Chris ▴ 20
1
vote
2
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871
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How to map geneIds to ENTREZIDs
Xenopus_laevis ChIPpeakAnno
23 months ago stacy.genovese • 0
1
vote
1
reply
792
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
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922
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Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
2.2 years ago michela ▴ 20
0
votes
1
reply
770
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
846
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
2.4 years ago mehdi • 0
0
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1
reply
885
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
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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
959
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.1 years ago Nadav • 0
1
vote
2
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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 • updated 3.1 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 4.3 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
replies
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
5.8 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
6.4 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
vote
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 7.7 years ago by ★ 1.3k • written 7.7 years ago by • 0
50 results • Page 1 of 1
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Comment: minfi latest update for EPIC V2 chip by macdonaldfrench7286566 • 0
Yes, the most updated analysis for the EPIC V2 chip using the minfi package still involves using the annotations provided by jokergoo. *Th…
Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
To compute CPM values from edgeR: ``` y <- DGEList(counts = counts, samples = samples, genes = genes, group = samples$Disease_status) y <- …
Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k
Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.
Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0
But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…
Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0
After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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