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ChIPpeakAnno
•
reset
1
vote
2
replies
88
views
How to map geneIds to ENTREZIDs
Xenopus_laevis
ChIPpeakAnno
3 days ago
stacy.genovese
• 0
1
vote
1
reply
153
views
Interpretation of $vennCounts output "Others"
ChIPpeakAnno
updated 6 weeks ago by
Ou, Jianhong
★ 1.3k • written 6 weeks ago by
cesar.arenasmena
▴ 10
0
votes
2
replies
185
views
Empty matrix
ChIPpeakAnno
Normalization
EnrichedHeatmap
HELP
TxDb.Celegans.UCSC.ce11.refGene
3 months ago
michela
▴ 20
0
votes
1
reply
163
views
Trying to understand the `select` option in `annotatePeakInBatch` function of `ChIPpeakAnno` package.
ChIPpeakAnno
updated 5 months ago by
James W. MacDonald
62k • written 5 months ago by
Mohan
• 0
1
vote
1
reply
188
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
6 months ago
mehdi
• 0
0
votes
1
reply
255
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno
ChIPSeq
updated 8 months ago by
Ou, Jianhong
★ 1.3k • written 8 months ago by
Abhilansh
• 0
0
votes
1
reply
326
views
peak annotation
ChIPpeakAnno
Annotation
updated 9 months ago by
Kai Hu
▴ 50 • written 10 months ago by
Bogdan
▴ 660
1
vote
2
replies
720
views
another problem when converting bed to granges using togranges
ChIPpeakAnno
11 months ago
Bakhtiyar
• 0
0
votes
2
replies
397
views
ChIP-seq or CUT&RUN enrichment
ChIPQC
ChIPpeakAnno
11 months ago
Bogdan
▴ 660
2
votes
6
replies
924
views
Problem converting a bed file to granges using togranges chippeakanno
ChIPpeakAnno
updated 12 months ago by
Kai Hu
▴ 50 • written 12 months ago by
Bakhtiyar
• 0
0
votes
0
replies
339
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks
ChIPpeakAnno
chipseq
14 months ago
Nadav
• 0
1
vote
2
replies
1.1k
views
ChIPpeakAnno findOverlapsOfPeaks error: "Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs."
HELP
ChIPpeakAnno
14 months ago
lexi.kellington
• 0
0
votes
4
replies
1.1k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
15 months ago
Tongjun
• 0
1
vote
6
replies
829
views
Annotation by CHIPeakAnno tool
ChIPpeakAnno
19 months ago
Arunima
▴ 10
1
vote
3
replies
526
views
genomicElementDistribution function not found
ChIPpeakAnno
updated 19 months ago by
Julie Zhu
★ 4.3k • written 19 months ago by
Arunima
▴ 10
2
votes
2
replies
809
views
Hello how to use ChIPpeakAnno for latest version of ensemble genome aligned data
ChIPpeakAnno
23 months ago
Lucky
• 0
7
votes
9
replies
1.1k
views
counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 2.4 years ago by
Julie Zhu
★ 4.3k • written 2.4 years ago by
C T
▴ 140
2
votes
2
replies
426
views
how to suppress makeVennDiagram plot
ChIPpeakAnno
2.5 years ago
C T
▴ 140
0
votes
2
replies
514
views
How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
ChIPpeakAnno
3.5 years ago
liruiradiant
• 0
0
votes
1
reply
657
views
Unable to annotate in ChIPQC using yeast genome
ChIPQC
GenomicRanges
ChIPpeakAnno
updated 21 months ago by
Zender
• 0 • written 3.7 years ago by
bertb
• 0
0
votes
4
replies
719
views
chippeakanno file reading error
ChiPpeakAnno
3.9 years ago
saddamhusain77
• 0
1
vote
6
replies
781
views
how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
4.0 years ago
ngs06
▴ 20
2
votes
10
replies
2.2k
views
ChIPpeakAnno, MACS format annotation
bioconductor
ChIPpeakAnno
updated 4.1 years ago by
Julie Zhu
★ 4.3k • written 5.9 years ago by
Khademul Islam
▴ 30
0
votes
7
replies
895
views
ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno
chipseq
R
updated 4.4 years ago by
Ou, Jianhong
★ 1.3k • written 4.4 years ago by
94133
• 0
3
votes
6
replies
997
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq
chippeakanno
chipseeker
4.5 years ago
94133
• 0
0
votes
1
reply
741
views
Error creating pool for permutation test (PeakPermTest)
permutation
pool
chippeakanno
4.5 years ago
ge2sasag
• 0
1
vote
1
reply
621
views
Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap
chippeakanno
updated 4.8 years ago by
Ou, Jianhong
★ 1.3k • written 4.8 years ago by
gdeniz
• 0
2
votes
2
replies
1.1k
views
Can't install ChIPpeakanno - "libmysqlclient was not found" - do I need to remove latest version of R?
ChIPpeakAnno
updated 5.0 years ago by
Mike Smith
★ 5.9k • written 5.0 years ago by
BioinfGuru
▴ 20
0
votes
3
replies
865
views
integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno
assignChromosomeRegion
updated 5.0 years ago by
Julie Zhu
★ 4.3k • written 5.0 years ago by
Janet Young
▴ 740
1
vote
1
reply
592
views
Custom regions in assignChromosomeRegion?
chippeakanno
updated 5.0 years ago by
Ou, Jianhong
★ 1.3k • written 5.0 years ago by
Roger
• 0
1
vote
2
replies
1.7k
views
Error : object path is not exported by namespace:Rsamtools
packages
installation problem
rsamtools
chippeakanno
ensembldb
5.1 years ago
inzirio
▴ 10
1
vote
4
replies
1.1k
views
ChIPpeakAnno binOverGene error
chippeakanno
binOverGene
updated 5.2 years ago by
Ou, Jianhong
★ 1.3k • written 5.2 years ago by
Wojeff
• 0
0
votes
1
reply
821
views
ChIPpeakAnno to find peaks nearest to miRNA
ChIPpeakAnno
ChIPpeakAnno
updated 5.3 years ago by
jun.yu
• 0 • written 10.2 years ago by
xyang2
▴ 120
2
votes
3
replies
2.1k
views
org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
chippeakanno
annotationdbi
updated 5.3 years ago by
jun.yu
• 0 • written 7.3 years ago by
Yi-Fang.Wang
• 0
0
votes
1
reply
908
views
featureAlignedSignal() error: deparse(sig): object 'sig' not found.
bioconductor
chippeakanno
featureAlignedDistribution
featureAlignedSignal
updated 5.3 years ago by
jun.yu
• 0 • written 6.4 years ago by
michael.alexander.finger
• 0
0
votes
1
reply
693
views
Help for ChIP script !! Error message while installing packages
annotation
chippeakanno
updated 5.3 years ago by
Martin Morgan
25k • written 5.3 years ago by
melissa.berto
• 0
5
votes
4
replies
3.3k
views
What are out-of-bound ranges? Is it necessary to get rid of them?
r
ChIPpeakAnno
5.8 years ago • updated 5.6 years ago
salamandra
▴ 20
4
votes
3
replies
894
views
Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 5.6 years ago by
Ou, Jianhong
★ 1.3k • written 5.6 years ago by
Haiying.Kong
▴ 110
1
vote
1
reply
785
views
Regarding ChIPpeakAnno installation error
chippeakanno
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
Neu.S
▴ 10
0
votes
3
replies
1.7k
views
ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is different than output of ol1$overlappingPeaks
chippeakanno
updated 5.8 years ago by
Ou, Jianhong
★ 1.3k • written 5.8 years ago by
sudhirjadhao2009
• 0
22
votes
10
replies
6.8k
views
Error in GRanges: could not find symbol "recursive" in environment of the generic function
granges
chippeakanno
updated 5.9 years ago by
davide.porcellato
▴ 10 • written 5.9 years ago by
deut13
▴ 80
2
votes
3
replies
1.1k
views
ChIPpeakAnno-annotation of peaklist with gene names, creating heat maps
chippeakanno
overlappingpeaks
annotation
updated 6.1 years ago by
Ou, Jianhong
★ 1.3k • written 6.1 years ago by
jmKeith
• 0
2
votes
7
replies
2.4k
views
ChIPpeakAnno-problem exporting data due to "arguments imply differing number of rows"
chippeakanno
updated 6.2 years ago by
Julie Zhu
★ 4.3k • written 6.2 years ago by
jmKeith
• 0
3
votes
5
replies
2.5k
views
Error with ChIPpeakAnno Ensembl annotation
ChIPpeakAnno
genomicfeatures
updated 6.2 years ago by
Julie Zhu
★ 4.3k • written 6.2 years ago by
b.nota
▴ 360
0
votes
1
reply
654
views
Discordant results in finding overlaps for three peak data with ChIPpeakAnno
ChIPpeakAnno
6.5 years ago
moyitasha
• 0
5
votes
15
replies
2.3k
views
nearest genes using TxDb.Hsapiens.UCSC.hg19
txdb.hsapiens.ucsc.hg19.knowngene
ChIPpeakAnno
updated 6.7 years ago by
Julie Zhu
★ 4.3k • written 6.7 years ago by
C T
▴ 140
0
votes
1
reply
868
views
Error with findOverlapsOfPeaks
ChIPpeakAnno
6.8 years ago
alex.tamburino
• 0
0
votes
3
replies
1.1k
views
CHiPpeakAnno GO and/or KEGG results presenting
chippeakanno
go
kegg
graphics
6.8 years ago
lokapal
• 0
0
votes
2
replies
1.8k
views
Help with toGRanges
granges
chippeakanno
updated 6.9 years ago by
Dario Strbenac
★ 1.5k • written 6.9 years ago by
mhartman3
• 0
0
votes
0
replies
986
views
count overlapping reads for CpG islands and annotate with gene names?
annotation
chippeakanno
rattus norvegicus
medip-seq
6.9 years ago
Vang Le
▴ 80
50 results • Page
1 of 1
Recent ...
Replies
Comment: mas5calls function doesn't work; mirna40cdf problem
by
Berna
• 0
Thank you for the information. I did not know that. Would you have a tip how I could proceed differently?
Comment: Correct use of Likelihood Ratio Test and LFC Shrinkage
by
ayabalbaa1990
• 0
Hi Michael, So I use this res_LRT <- results(dds_lrt) r2=lfcShrink(dds_lrt, coef=7, res=res_LRT) tu run lfcshrink with LRT, is that oko?…
Comment: Combat and dds Object
by
shaimaa
• 0
I used the combat-seq but the deseq complain as its not integer what should i do
Answer: Different summary() and results() values in DeSeq2
by
Basti
▴ 540
summary() tells you the number of genes with low counts, see independant filtering of results in the DESeq2 vignette : https://www.biocondu…
Comment: Atena package - error (new user)
by
beatriz.calvo
▴ 30
Hi Lalani, We have fixed the bug that lead to the error. The new version of the package (with the bug fixed) will be available in 24-48h. …
Votes
Answer: mas5calls function doesn't work; mirna40cdf problem
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
A: How to translate FASTA file of DNA sequence to protein sequence using Biostrings
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