Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
ChIPseeker
•
reset
0
votes
1
reply
62
views
ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
2 days ago • updated 3 hours ago
Gyan Prakash Mishra
• 0
0
votes
0
replies
62
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq
ChIPseeker
23 days ago
Swadha
• 0
0
votes
0
replies
63
views
What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
7 weeks ago
hyjforesight
• 0
0
votes
1
reply
509
views
ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
6 months ago
william.ho
• 0
0
votes
2
replies
291
views
getPromoters
ChIPseeker
7 months ago
guoyou88
• 0
0
votes
0
replies
227
views
ChIPseeker, how to customize plotDistToTSS
ChIPseeker
7 months ago
alexandre.blais
▴ 50
1
vote
3
replies
282
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
11 months ago • updated 10 months ago
Meghna
• 0
0
votes
0
replies
225
views
CHIPseeker- promoter gene names
ChIPseeker
CHIPsee
11 months ago
rb
• 0
0
votes
1
reply
327
views
ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 13 months ago by
Sam
▴ 10 • written 13 months ago by
ikumar2000
• 0
0
votes
0
replies
225
views
What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
13 months ago
Sam
▴ 10
0
votes
0
replies
307
views
Annotation of downstream in ChIPseeker
downstream
Priority
ChIPseeker
13 months ago
Xiaojie Cheng
• 0
0
votes
2
replies
462
views
ChIPseeker failing on r-devel on CRAN checks
ChIPseeker
cinaR
14 months ago
Onur Karakaslar
• 0
1
vote
4
replies
507
views
Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker
TxDb.Mmusculus.UCSC.mm10.knownGene
15 months ago
Kasit
• 0
0
votes
0
replies
195
views
ChIPSeeker covplot function, fix yaxis
ChIPseeker
16 months ago
jordi.planells
• 0
0
votes
0
replies
251
views
Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
18 months ago • updated 17 months ago
Sam
▴ 10
2
votes
2
replies
1.2k
views
ChIP seeker annotation error
DiffBind
chipseq
ChIPseeker
ChipDb
annotation
18 months ago • updated 15 months ago
Mar Mar
▴ 20
5
votes
3
replies
428
views
importing BED with non-integer values
ChIPseeker
ChIPSeqData
updated 18 months ago by
James W. MacDonald
59k • written 18 months ago by
Morris
• 0
0
votes
0
replies
194
views
Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
18 months ago
Prasoon
• 0
0
votes
1
reply
433
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR
ChIPs
ChIPseeker
ChIPSeq
chipseq
updated 18 months ago by
James W. MacDonald
59k • written 18 months ago by
ret28
• 0
0
votes
0
replies
332
views
About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
19 months ago
ahua217
▴ 10
0
votes
0
replies
320
views
How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
19 months ago
bioinfouser2
▴ 10
0
votes
1
reply
599
views
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker
plotAnnoPie
20 months ago
amafon95
• 0
0
votes
0
replies
294
views
p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
21 months ago
mwong043
• 0
0
votes
0
replies
350
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker
TxDb
getpromoters
software error
2.0 years ago
hfyuan2016
• 0
0
votes
0
replies
267
views
Potential oversimplification in the overlap function
ChIPseeker
2.0 years ago
konsta.kukkonen
• 0
1
vote
0
replies
311
views
Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
2.0 years ago
egbastakis
• 0
0
votes
1
reply
652
views
ChIPSeeker with Ensembl IDs
chipseeker
Ensembl
EnsDb.Mmusculus.v79
ensembldb
2.1 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
403
views
ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
2.3 years ago
Guandong Shang
▴ 20
0
votes
1
reply
564
views
Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
2.7 years ago
sutturka
• 0
1
vote
2
replies
2.4k
views
Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq
ChIPseeker
peak annotation
annotatePeak()
Diffbind
2.7 years ago
researcher
• 0
2
votes
1
reply
1.2k
views
Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker
ChIPseeker
2.7 years ago
endrebak85
▴ 30
1
vote
3
replies
497
views
Error: package or namespace load failed for 'ChIPseeker': 'TxDb.Hsapiens.UCSC.hg19.knownGene' is not exported from 'namespace: TxDb.Hsapiens.UCSC.hg1…
chipseq
chipseeker
R
Bioconductor
updated 2.9 years ago by
Martin Morgan
25k • written 2.9 years ago by
charlesgwellem
▴ 10
0
votes
1
reply
1.2k
views
error in readPeakFile {chipseeker}
ChIPseeker
readPeakFile
3.0 years ago
theodore.georgomanolis
• 0
0
votes
1
reply
558
views
Problem in using covplot ChIPseeker
ChIPseeker
software error
3.2 years ago
vasudha.sharma
• 0
3
votes
2
replies
864
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges
ChIPseeker
annotatePeak
TxDb
EnsDb
updated 3.3 years ago by
Johannes Rainer
★ 1.9k • written 3.3 years ago by
foehn
▴ 80
1
vote
1
reply
849
views
ChIPseeker genomicAnnotationPriority
annotation
chipseeker
updated 10 months ago by
hqlkjx
• 0 • written 3.4 years ago by
dolata
▴ 10
0
votes
0
replies
636
views
How to use ChIPseeker for getting genebody annotations.
chipseeker
chipseq
3.4 years ago
bioinfouser2
▴ 10
0
votes
2
replies
648
views
how to get frequencies from plotDistToTSS
chipseeker
3.4 years ago
KKO
• 0
1
vote
0
replies
522
views
ChipSeeker Flanking gene annotation
chipseeker
3.6 years ago
Lauma R
▴ 10
3
votes
4
replies
1.1k
views
ChIPseeker/Question about ''annoatePeak' function and for Bioconductor AnnotationData Packages for L.japonicus
chipseeker
Bioconductor AnnotationData Packages
Lotus japonicus
ChIPseq
updated 3.6 years ago by
James W. MacDonald
59k • written 3.6 years ago by
egbastakis
• 0
0
votes
0
replies
437
views
covplot and getChrCov function
chipseeker
3.6 years ago
xiaofeiwang198266
• 0
1
vote
3
replies
882
views
How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker
chipseq
updated 3.7 years ago by
Guangchuang Yu
★ 1.2k • written 3.8 years ago by
bioinfouser2
▴ 10
0
votes
0
replies
452
views
How to get the genome distribution in proportion of promoter, 1st exon, other exon, 1st intron, other intron, distal intergenic, etc from a species
chipseeker
3.7 years ago
bright602
• 0
3
votes
6
replies
834
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq
chippeakanno
chipseeker
3.8 years ago
94133
• 0
1
vote
1
reply
1.5k
views
Error: package or namespace load failed for 'ChIPseeker' in dyn.load(file, DLLpath = DLLpath
chipseeker
3.9 years ago
liucz200904
• 0
0
votes
1
reply
543
views
How does vennplot() within Chipseeker define overlaps?
chipseeker
vennplot
3.9 years ago
kevin.potter12
• 0
0
votes
1
reply
446
views
Error in getGenomicAnnoStat(peak.gr) : object 'plab' not found
ChIPseeker
updated 4.1 years ago by
Guangchuang Yu
★ 1.2k • written 4.1 years ago by
chenkehua4803
• 0
0
votes
3
replies
1.1k
views
"input object should be a named list" error in ChIPseeker
ChIPseeker
named list error
plotAnnoBar
plotDistToTSS
vennplot
updated 4.2 years ago by
Guangchuang Yu
★ 1.2k • written 4.2 years ago by
k.panov
• 0
0
votes
0
replies
704
views
problem on getpromoters on hg38
chipseeker
ChIPseeker
4.2 years ago
jarod_v6@libero.it
▴ 40
0
votes
3
replies
999
views
custom background list for ReactomePA
reactomepa
chipseeker
Guangchuang Yu
4.4 years ago
andrew.gehrke
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: R: problem with running time-series analysis software: Mfuzz
by
Kevin Blighe
3.5k
Cross-posted: https://www.biostars.org/p/9524023/
Comment: ROC plot for OPLS-DA
by
Eddie
• 0
Hi, That was helpful. Thank you. How to do the same for the testing data?
Comment: ChIP-seq peak annotation to gene in ChIPseeker
by
Gyan Prakash Mishra
• 0
After going through the package, I think all the peaks are annotated to genes irrespective of distance to TSS. There is also another functi…
Comment: lpsymphony compilation trouble
by
Cankun
• 0
It's 2022 and it still works for lpsymphony_1.24.0
Comment: UniprotKB AC/ID to Entrez ID Conversion
by
James W. MacDonald
59k
I fixed this when Bioc 3.13 was the release version, so it should work in 3.14 and the current release. ``` > up <- UniProt.ws() > input …
Votes
A: lpsymphony compilation trouble
Answer: Robust Multi-array Average could get negative value or not?
Answer: Robust Multi-array Average could get negative value or not?
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Awards
• All
Scholar
to
James W. MacDonald
59k
Scholar
to
Guido Hooiveld
★ 3.2k
Scholar
to
Kevin Blighe
3.5k
Scholar
to
SamGG
▴ 270
Prophet
to
johnmcma
▴ 10
Locations
• All
WEHI, Melbourne, Australia,
53 minutes ago
Republic of Ireland,
1 hour ago
Belgium,
1 hour ago
China,
1 hour ago
United States,
2 hours ago
Traffic: 388 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6