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ChiPpeakAnno
•
reset
0
votes
0
replies
100
views
Best method for annotating distal peaks
ChIPSeq
annotation
ChIPpeakAnno
7 weeks ago
nilanjanamani88
• 0
1
vote
5
replies
480
views
ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
5 months ago
ilaria.maurizio
• 0
0
votes
0
replies
252
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno
ChIPSeq
MotifDiscovery
6 months ago
franciscrick41
• 0
3
votes
7
replies
792
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 6 months ago by
Chris
• 0
2
votes
14
replies
1.0k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno
ChIPSeq
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
Jerina
▴ 10
0
votes
1
reply
447
views
genomeStyles error in ChIPpeakAnno
Chippeakanno
ChIPpeakAnno
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
Tami
• 0
0
votes
2
replies
558
views
annotate peaks using a custom genome
ChIPSeq
annotate
ChIPpeakAnno
updated 11 months ago by
Kai Hu
▴ 70 • written 11 months ago by
C T
▴ 140
9
votes
16
replies
1.5k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
11 months ago
Chris
• 0
1
vote
2
replies
585
views
How to map geneIds to ENTREZIDs
Xenopus_laevis
ChIPpeakAnno
14 months ago
stacy.genovese
• 0
1
vote
1
reply
576
views
Interpretation of $vennCounts output "Others"
ChIPpeakAnno
updated 15 months ago by
Ou, Jianhong
★ 1.3k • written 15 months ago by
cesar.arenasmena
▴ 10
0
votes
2
replies
685
views
Empty matrix
ChIPpeakAnno
Normalization
EnrichedHeatmap
HELP
TxDb.Celegans.UCSC.ce11.refGene
17 months ago
michela
▴ 20
0
votes
1
reply
557
views
Trying to understand the `select` option in `annotatePeakInBatch` function of `ChIPpeakAnno` package.
ChIPpeakAnno
updated 19 months ago by
James W. MacDonald
65k • written 19 months ago by
Mohan
• 0
1
vote
1
reply
595
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
20 months ago
mehdi
• 0
0
votes
1
reply
678
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno
ChIPSeq
updated 22 months ago by
Ou, Jianhong
★ 1.3k • written 22 months ago by
Abhilansh
• 0
0
votes
1
reply
738
views
peak annotation
ChIPpeakAnno
Annotation
updated 23 months ago by
Kai Hu
▴ 70 • written 2.0 years ago by
Bogdan
▴ 670
1
vote
2
replies
1.6k
views
another problem when converting bed to granges using togranges
ChIPpeakAnno
2.1 years ago
Bakhtiyar
• 0
0
votes
2
replies
840
views
ChIP-seq or CUT&RUN enrichment
ChIPQC
ChIPpeakAnno
2.1 years ago
Bogdan
▴ 670
2
votes
6
replies
2.0k
views
Problem converting a bed file to granges using togranges chippeakanno
ChIPpeakAnno
updated 2.1 years ago by
Kai Hu
▴ 70 • written 2.1 years ago by
Bakhtiyar
• 0
0
votes
0
replies
705
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks
ChIPpeakAnno
chipseq
2.3 years ago
Nadav
• 0
1
vote
2
replies
2.3k
views
ChIPpeakAnno findOverlapsOfPeaks error: "Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs."
HELP
ChIPpeakAnno
2.4 years ago
lexi.kellington
• 0
0
votes
4
replies
2.0k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
2.4 years ago
Tongjun
• 0
1
vote
6
replies
1.5k
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
2.8 years ago • updated 2.7 years ago
Arunima
▴ 10
1
vote
3
replies
873
views
genomicElementDistribution function not found
ChIPpeakAnno
updated 2.8 years ago by
Julie Zhu
★ 4.3k • written 2.8 years ago by
Arunima
▴ 10
2
votes
2
replies
1.2k
views
Hello how to use ChIPpeakAnno for latest version of ensemble genome aligned data
ChIPpeakAnno
3.1 years ago
Lucky
• 0
7
votes
9
replies
1.8k
views
counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 3.6 years ago by
Julie Zhu
★ 4.3k • written 3.6 years ago by
C T
▴ 140
2
votes
2
replies
767
views
how to suppress makeVennDiagram plot
ChIPpeakAnno
3.6 years ago
C T
▴ 140
1
vote
2
replies
925
views
How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
ChIPpeakAnno
4.7 years ago
liruiradiant
• 0
0
votes
1
reply
1.1k
views
Unable to annotate in ChIPQC using yeast genome
ChIPQC
GenomicRanges
ChIPpeakAnno
updated 2.9 years ago by
Zender
• 0 • written 4.9 years ago by
bertb
• 0
0
votes
4
replies
1.2k
views
chippeakanno file reading error
ChiPpeakAnno
5.0 years ago
saddamhusain77
• 0
1
vote
6
replies
1.3k
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
5.1 years ago
ngs06
▴ 20
2
votes
10
replies
3.2k
views
ChIPpeakAnno, MACS format annotation
bioconductor
ChIPpeakAnno
updated 5.2 years ago by
Julie Zhu
★ 4.3k • written 7.0 years ago by
Khademul Islam
▴ 30
0
votes
7
replies
1.5k
views
ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno
chipseq
R
updated 5.5 years ago by
Ou, Jianhong
★ 1.3k • written 5.5 years ago by
94133
• 0
3
votes
6
replies
1.6k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq
chippeakanno
chipseeker
5.7 years ago
94133
• 0
0
votes
1
reply
1.1k
views
Error creating pool for permutation test (PeakPermTest)
permutation
pool
chippeakanno
5.7 years ago
ge2sasag
• 0
1
vote
1
reply
918
views
Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap
chippeakanno
updated 5.9 years ago by
Ou, Jianhong
★ 1.3k • written 5.9 years ago by
gdeniz
• 0
2
votes
2
replies
1.6k
views
Can't install ChIPpeakanno - "libmysqlclient was not found" - do I need to remove latest version of R?
ChIPpeakAnno
updated 6.1 years ago by
Mike Smith
★ 6.5k • written 6.1 years ago by
BioinfGuru
▴ 20
0
votes
3
replies
1.3k
views
integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno
assignChromosomeRegion
updated 6.1 years ago by
Julie Zhu
★ 4.3k • written 6.1 years ago by
Janet Young
▴ 740
1
vote
1
reply
911
views
Custom regions in assignChromosomeRegion?
chippeakanno
updated 6.2 years ago by
Ou, Jianhong
★ 1.3k • written 6.2 years ago by
Roger
• 0
1
vote
2
replies
2.3k
views
Error : object path is not exported by namespace:Rsamtools
packages
installation problem
rsamtools
chippeakanno
ensembldb
6.3 years ago
inzirio
▴ 10
1
vote
4
replies
1.5k
views
ChIPpeakAnno binOverGene error
chippeakanno
binOverGene
updated 6.3 years ago by
Ou, Jianhong
★ 1.3k • written 6.3 years ago by
Wojeff
• 0
0
votes
1
reply
1.1k
views
ChIPpeakAnno to find peaks nearest to miRNA
ChIPpeakAnno
ChIPpeakAnno
updated 6.4 years ago by
jun.yu
• 0 • written 11.3 years ago by
xyang2
▴ 120
2
votes
3
replies
2.6k
views
org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
chippeakanno
annotationdbi
updated 6.4 years ago by
jun.yu
• 0 • written 8.4 years ago by
Yi-Fang.Wang
• 0
0
votes
1
reply
1.3k
views
featureAlignedSignal() error: deparse(sig): object 'sig' not found.
bioconductor
chippeakanno
featureAlignedDistribution
featureAlignedSignal
updated 6.4 years ago by
jun.yu
• 0 • written 7.5 years ago by
michael.alexander.finger
• 0
0
votes
1
reply
927
views
Help for ChIP script !! Error message while installing packages
annotation
chippeakanno
updated 6.5 years ago by
Martin Morgan
25k • written 6.5 years ago by
melissa.berto
• 0
5
votes
4
replies
4.6k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r
ChIPpeakAnno
7.0 years ago • updated 6.7 years ago
salamandra
▴ 20
4
votes
3
replies
1.3k
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 6.8 years ago by
Ou, Jianhong
★ 1.3k • written 6.8 years ago by
Haiying.Kong
▴ 110
1
vote
1
reply
1.1k
views
Regarding ChIPpeakAnno installation error
chippeakanno
updated 6.9 years ago by
Martin Morgan
25k • written 6.9 years ago by
Neu.S
▴ 10
0
votes
3
replies
2.4k
views
ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is different than output of ol1$overlappingPeaks
chippeakanno
updated 7.0 years ago by
Ou, Jianhong
★ 1.3k • written 7.0 years ago by
sudhirjadhao2009
• 0
22
votes
10
replies
7.4k
views
Error in GRanges: could not find symbol "recursive" in environment of the generic function
granges
chippeakanno
updated 7.0 years ago by
davide.porcellato
▴ 10 • written 7.1 years ago by
deut13
▴ 80
2
votes
3
replies
1.5k
views
ChIPpeakAnno-annotation of peaklist with gene names, creating heat maps
chippeakanno
overlappingpeaks
annotation
updated 7.3 years ago by
Ou, Jianhong
★ 1.3k • written 7.3 years ago by
jmKeith
• 0
50 results • Page
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Recent ...
Replies
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
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