Showing : chippeakanno • reset
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
11 weeks ago nilanjanamani88 • 0
1
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5
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545
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ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
6 months ago ilaria.maurizio • 0
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0
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274
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
7 months ago franciscrick41 • 0
3
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7
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838
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
2
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14
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1.1k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 8 months ago by 65k • written 8 months ago by ▴ 10
0
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1
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476
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genomeStyles error in ChIPpeakAnno
Chippeakanno ChIPpeakAnno
updated 9 months ago by 65k • written 9 months ago by • 0
0
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2
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592
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 12 months ago by ▴ 70 • written 12 months ago by ▴ 140
9
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16
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1.6k
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How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
12 months ago Chris • 0
1
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2
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622
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How to map geneIds to ENTREZIDs
Xenopus_laevis ChIPpeakAnno
15 months ago stacy.genovese • 0
1
vote
1
reply
598
views
Interpretation of $vennCounts output "Others"
ChIPpeakAnno
updated 16 months ago by ★ 1.3k • written 16 months ago by ▴ 10
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2
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710
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Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
18 months ago michela ▴ 20
0
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1
reply
577
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Trying to understand the `select` option in `annotatePeakInBatch` function of `ChIPpeakAnno` package.
ChIPpeakAnno
updated 20 months ago by 65k • written 20 months ago by • 0
1
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1
reply
622
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
20 months ago mehdi • 0
0
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1
reply
699
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 23 months ago by ★ 1.3k • written 23 months ago by • 0
0
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1
reply
787
views
peak annotation
ChIPpeakAnno Annotation
updated 2.0 years ago by ▴ 70 • written 2.1 years ago by ▴ 670
1
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2
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1.6k
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another problem when converting bed to granges using togranges
ChIPpeakAnno
2.2 years ago Bakhtiyar • 0
0
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2
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885
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ChIP-seq or CUT&RUN enrichment
ChIPQC ChIPpeakAnno
2.2 years ago Bogdan ▴ 670
2
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6
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2.1k
views
Problem converting a bed file to granges using togranges chippeakanno
ChIPpeakAnno
updated 2.2 years ago by ▴ 70 • written 2.2 years ago by • 0
0
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0
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733
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.4 years ago Nadav • 0
1
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2
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2.4k
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ChIPpeakAnno findOverlapsOfPeaks error: "Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs."
HELP ChIPpeakAnno
2.5 years ago lexi.kellington • 0
0
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4
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2.1k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
2.5 years ago Tongjun • 0
1
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6
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1.5k
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
2.8 years ago Arunima ▴ 10
1
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3
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904
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genomicElementDistribution function not found
ChIPpeakAnno
updated 2.8 years ago by ★ 4.3k • written 2.8 years ago by ▴ 10
2
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2
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1.3k
views
Hello how to use ChIPpeakAnno for latest version of ensemble genome aligned data
ChIPpeakAnno
3.1 years ago Lucky • 0
7
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9
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1.8k
views
counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 3.6 years ago by ★ 4.3k • written 3.7 years ago by ▴ 140
2
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2
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794
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how to suppress makeVennDiagram plot
ChIPpeakAnno
3.7 years ago C T ▴ 140
1
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2
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949
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How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
ChIPpeakAnno
4.7 years ago liruiradiant • 0
0
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1
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1.1k
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Unable to annotate in ChIPQC using yeast genome
ChIPQC GenomicRanges ChIPpeakAnno
updated 3.0 years ago by • 0 • written 4.9 years ago by • 0
0
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4
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1.2k
views
chippeakanno file reading error
ChiPpeakAnno
5.1 years ago saddamhusain77 • 0
1
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6
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1.3k
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
5.2 years ago ngs06 ▴ 20
2
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10
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3.2k
views
ChIPpeakAnno, MACS format annotation
bioconductor ChIPpeakAnno
updated 5.3 years ago by ★ 4.3k • written 7.1 years ago by ▴ 30
0
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7
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1.5k
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ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 5.6 years ago by ★ 1.3k • written 5.6 years ago by • 0
3
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6
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1.6k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
5.8 years ago 94133 • 0
0
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1
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1.1k
views
Error creating pool for permutation test (PeakPermTest)
permutation pool chippeakanno
5.8 years ago ge2sasag • 0
1
vote
1
reply
954
views
Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap chippeakanno
updated 6.0 years ago by ★ 1.3k • written 6.0 years ago by • 0
2
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2
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1.6k
views
Can't install ChIPpeakanno - "libmysqlclient was not found" - do I need to remove latest version of R?
ChIPpeakAnno
updated 6.2 years ago by ★ 6.5k • written 6.2 years ago by ▴ 30
0
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3
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1.3k
views
integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno assignChromosomeRegion
updated 6.2 years ago by ★ 4.3k • written 6.2 years ago by ▴ 740
1
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1
reply
931
views
Custom regions in assignChromosomeRegion?
chippeakanno
updated 6.2 years ago by ★ 1.3k • written 6.2 years ago by • 0
1
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2
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2.4k
views
Error : object path is not exported by namespace:Rsamtools
packages installation problem rsamtools chippeakanno ensembldb
6.4 years ago inzirio ▴ 10
1
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4
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1.5k
views
ChIPpeakAnno binOverGene error
chippeakanno binOverGene
updated 6.4 years ago by ★ 1.3k • written 6.4 years ago by • 0
0
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1
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1.1k
views
ChIPpeakAnno to find peaks nearest to miRNA
ChIPpeakAnno ChIPpeakAnno
updated 6.5 years ago by • 0 • written 11.4 years ago by ▴ 120
2
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3
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2.7k
views
org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
chippeakanno annotationdbi
updated 6.5 years ago by • 0 • written 8.5 years ago by • 0
0
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1
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1.3k
views
featureAlignedSignal() error: deparse(sig): object 'sig' not found.
bioconductor chippeakanno featureAlignedDistribution featureAlignedSignal
updated 6.5 years ago by • 0 • written 7.6 years ago by • 0
0
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1
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945
views
Help for ChIP script !! Error message while installing packages
annotation chippeakanno
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
5
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4
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4.7k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r ChIPpeakAnno
7.0 years ago • updated 6.8 years ago salamandra ▴ 20
4
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3
replies
1.3k
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 6.8 years ago by ★ 1.3k • written 6.8 years ago by ▴ 110
1
vote
1
reply
1.1k
views
Regarding ChIPpeakAnno installation error
chippeakanno
updated 7.0 years ago by 25k • written 7.0 years ago by ▴ 10
0
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3
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2.4k
views
ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is different than output of ol1$overlappingPeaks
chippeakanno
updated 7.1 years ago by ★ 1.3k • written 7.1 years ago by • 0
22
votes
10
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7.4k
views
Error in GRanges: could not find symbol "recursive" in environment of the generic function
granges chippeakanno
updated 7.1 years ago by ▴ 10 • written 7.1 years ago by ▴ 80
2
votes
3
replies
1.6k
views
ChIPpeakAnno-annotation of peaklist with gene names, creating heat maps
chippeakanno overlappingpeaks annotation
updated 7.4 years ago by ★ 1.3k • written 7.4 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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