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Showing :
chippeakanno
•
reset
0
votes
3
replies
557
views
ChIPpeakAnno can not load data
genomes
ChIPpeakAnno
written 6 months ago by
文杰
• 0
0
votes
0
replies
625
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
10 months ago
Raghad
• 0
0
votes
0
replies
590
views
Best method for annotating distal peaks
ChIPSeq
annotation
ChIPpeakAnno
13 months ago
nilanjanamani88
• 0
1
vote
5
replies
1.3k
views
ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
17 months ago
ilaria.maurizio
• 0
0
votes
0
replies
562
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno
ChIPSeq
MotifDiscovery
18 months ago
franciscrick41
• 0
3
votes
7
replies
1.5k
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 18 months ago by
Chris
▴ 20
2
votes
14
replies
1.9k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno
ChIPSeq
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Jerina
▴ 10
0
votes
1
reply
805
views
genomeStyles error in ChIPpeakAnno
Chippeakanno
ChIPpeakAnno
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Tami
• 0
0
votes
2
replies
1.0k
views
annotate peaks using a custom genome
ChIPSeq
annotate
ChIPpeakAnno
updated 23 months ago by
Kai Hu
▴ 70 • written 23 months ago by
C T
▴ 140
9
votes
16
replies
2.5k
views
How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
23 months ago
Chris
▴ 20
1
vote
2
replies
943
views
How to map geneIds to ENTREZIDs
Xenopus_laevis
ChIPpeakAnno
2.1 years ago
stacy.genovese
• 0
1
vote
1
reply
850
views
Interpretation of $vennCounts output "Others"
ChIPpeakAnno
updated 2.2 years ago by
Ou, Jianhong
★ 1.3k • written 2.2 years ago by
cesar.arenasmena
▴ 10
0
votes
2
replies
975
views
Empty matrix
ChIPpeakAnno
Normalization
EnrichedHeatmap
HELP
TxDb.Celegans.UCSC.ce11.refGene
2.4 years ago
michela
▴ 20
0
votes
1
reply
840
views
Trying to understand the `select` option in `annotatePeakInBatch` function of `ChIPpeakAnno` package.
ChIPpeakAnno
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
Mohan
• 0
1
vote
1
reply
927
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
2.6 years ago
mehdi
• 0
0
votes
1
reply
932
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno
ChIPSeq
updated 2.8 years ago by
Ou, Jianhong
★ 1.3k • written 2.9 years ago by
Abhilansh
• 0
0
votes
1
reply
1.1k
views
peak annotation
ChIPpeakAnno
Annotation
updated 2.9 years ago by
Kai Hu
▴ 70 • written 3.0 years ago by
Bogdan
▴ 670
1
vote
2
replies
2.1k
views
another problem when converting bed to granges using togranges
ChIPpeakAnno
3.1 years ago
Bakhtiyar
• 0
0
votes
2
replies
1.2k
views
ChIP-seq or CUT&RUN enrichment
ChIPQC
ChIPpeakAnno
3.1 years ago
Bogdan
▴ 670
2
votes
6
replies
3.2k
views
Problem converting a bed file to granges using togranges chippeakanno
ChIPpeakAnno
updated 3.1 years ago by
Kai Hu
▴ 70 • written 3.1 years ago by
Bakhtiyar
• 0
0
votes
0
replies
1.0k
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks
ChIPpeakAnno
chipseq
3.3 years ago
Nadav
• 0
1
vote
2
replies
3.1k
views
ChIPpeakAnno findOverlapsOfPeaks error: "Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs."
HELP
ChIPpeakAnno
3.4 years ago
lexi.kellington
• 0
0
votes
4
replies
2.6k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
3.4 years ago
Tongjun
• 0
1
vote
6
replies
2.0k
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
3.7 years ago
Arunima
▴ 10
1
vote
3
replies
1.2k
views
genomicElementDistribution function not found
ChIPpeakAnno
updated 3.7 years ago by
Julie Zhu
★ 4.3k • written 3.7 years ago by
Arunima
▴ 10
2
votes
2
replies
1.7k
views
Hello how to use ChIPpeakAnno for latest version of ensemble genome aligned data
ChIPpeakAnno
4.0 years ago
Lucky
• 0
7
votes
9
replies
2.6k
views
counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 4.6 years ago by
Julie Zhu
★ 4.3k • written 4.6 years ago by
C T
▴ 140
2
votes
2
replies
1.1k
views
how to suppress makeVennDiagram plot
ChIPpeakAnno
4.6 years ago
C T
▴ 140
1
vote
2
replies
1.2k
views
How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
ChIPpeakAnno
5.6 years ago
liruiradiant
• 0
0
votes
1
reply
1.4k
views
Unable to annotate in ChIPQC using yeast genome
ChIPQC
GenomicRanges
ChIPpeakAnno
updated 3.9 years ago by
Zender
• 0 • written 5.9 years ago by
bertb
• 0
0
votes
4
replies
1.6k
views
chippeakanno file reading error
ChiPpeakAnno
6.0 years ago
saddamhusain77
• 0
1
vote
6
replies
1.7k
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
6.1 years ago
ngs06
▴ 20
2
votes
10
replies
3.9k
views
ChIPpeakAnno, MACS format annotation
bioconductor
ChIPpeakAnno
updated 6.2 years ago by
Julie Zhu
★ 4.3k • written 8.0 years ago by
Khademul Islam
▴ 30
0
votes
7
replies
1.9k
views
ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno
chipseq
R
updated 6.5 years ago by
Ou, Jianhong
★ 1.3k • written 6.5 years ago by
94133
• 0
3
votes
6
replies
2.0k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq
chippeakanno
chipseeker
6.7 years ago
94133
• 0
0
votes
1
reply
1.4k
views
Error creating pool for permutation test (PeakPermTest)
permutation
pool
chippeakanno
6.7 years ago
ge2sasag
• 0
1
vote
1
reply
1.2k
views
Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap
chippeakanno
updated 6.9 years ago by
Ou, Jianhong
★ 1.3k • written 6.9 years ago by
gdeniz
• 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 7.1 years ago by
Mike Smith
★ 6.6k • written 7.1 years ago by
BioinfGuru
▴ 70
0
votes
3
replies
1.7k
views
integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno
assignChromosomeRegion
updated 7.1 years ago by
Julie Zhu
★ 4.3k • written 7.1 years ago by
Janet Young
▴ 740
1
vote
1
reply
1.2k
views
Custom regions in assignChromosomeRegion?
chippeakanno
updated 7.1 years ago by
Ou, Jianhong
★ 1.3k • written 7.1 years ago by
Roger
• 0
1
vote
2
replies
2.8k
views
Error : object path is not exported by namespace:Rsamtools
packages
installation problem
rsamtools
chippeakanno
ensembldb
7.3 years ago
inzirio
▴ 10
1
vote
4
replies
1.8k
views
ChIPpeakAnno binOverGene error
chippeakanno
binOverGene
updated 7.3 years ago by
Ou, Jianhong
★ 1.3k • written 7.3 years ago by
Wojeff
• 0
0
votes
1
reply
1.4k
views
ChIPpeakAnno to find peaks nearest to miRNA
ChIPpeakAnno
ChIPpeakAnno
updated 7.4 years ago by
jun.yu
• 0 • written 12.3 years ago by
xyang2
▴ 120
2
votes
3
replies
3.0k
views
org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
chippeakanno
annotationdbi
updated 7.4 years ago by
jun.yu
• 0 • written 9.4 years ago by
Yi-Fang.Wang
• 0
0
votes
1
reply
1.6k
views
featureAlignedSignal() error: deparse(sig): object 'sig' not found.
bioconductor
chippeakanno
featureAlignedDistribution
featureAlignedSignal
updated 7.4 years ago by
jun.yu
• 0 • written 8.5 years ago by
michael.alexander.finger
• 0
0
votes
1
reply
1.2k
views
Help for ChIP script !! Error message while installing packages
annotation
chippeakanno
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
melissa.berto
• 0
5
votes
4
replies
5.5k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r
ChIPpeakAnno
7.9 years ago • updated 7.7 years ago
salamandra
▴ 20
4
votes
3
replies
1.6k
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 7.8 years ago by
Ou, Jianhong
★ 1.3k • written 7.8 years ago by
Haiying.Kong
▴ 110
1
vote
1
reply
1.4k
views
Regarding ChIPpeakAnno installation error
chippeakanno
updated 7.9 years ago by
Martin Morgan
25k • written 7.9 years ago by
Neu.S
▴ 10
0
votes
3
replies
3.0k
views
ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is different than output of ol1$overlappingPeaks
chippeakanno
updated 8.0 years ago by
Ou, Jianhong
★ 1.3k • written 8.0 years ago by
sudhirjadhao2009
• 0
50 results • Page
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Comment: DiffBind custom normalization factor
by
Abbie
• 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
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I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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