Showing : Chippeakanno • reset
0
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3
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476
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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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539
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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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539
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
12 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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520
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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
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1.8k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 17 months ago by 67k • written 17 months ago by ▴ 10
0
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1
reply
755
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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953
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 21 months ago by ▴ 70 • written 21 months ago by ▴ 140
9
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16
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2.3k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
22 months ago • updated 21 months ago Chris ▴ 20
1
vote
2
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901
views
How to map geneIds to ENTREZIDs
Xenopus_laevis ChIPpeakAnno
2.0 years ago stacy.genovese • 0
1
vote
1
reply
815
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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947
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
793
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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
876
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
2.5 years ago mehdi • 0
0
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1
reply
906
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
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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
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.2 years ago Nadav • 0
1
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2
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3.0k
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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
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4
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2.5k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
3.3 years ago • updated 3.2 years ago Tongjun • 0
1
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6
replies
2.0k
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
3.6 years ago Arunima ▴ 10
1
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3
replies
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
votes
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
5.9 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 6.1 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 6.4 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
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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
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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 12.2 years ago by ▴ 120
2
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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 7.6 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 7.8 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 7.8 years ago by ★ 1.3k • written 7.8 years ago by • 0
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Comment: plyranges: find exact GRanges match keeping metadata columns by alexis.weinreb • 0
Thank you, this does clarify the available options.
Answer: displaying the differential expression with deseq2 over 4X2 samples with the in by James W. MacDonald 67k
If you have paired data you should block on subject, which is algebraically the same as fitting a model on the difference between treated a…
Answer: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by jodan • 0
Your approach sounds solid! You might also consider plotting a scatter plot comparing log2 fold changes from both datasets to identify gene…
Answer: Unused arguments error without used arguments in GSVA? by jodan • 0
It looks like the ssgseaParam function might not be passing the correct parameters to GSVA::gsva(). The error suggests that minSize and max…
Answer: Using genomicRanges / plyranges to calculate score of peaks within intervals by Michael Love 43k
This should be possible with plyranges using `join_overlap` and `group_by` on the metadata from the tile. E.g. create `tile.id` as a variab…
Votes
Answer: Find exact GRanges match keeping metadata columns
Answer: Find exact GRanges match keeping metadata columns
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
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