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chiPseeker
•
reset
0
votes
0
replies
71
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
20 days ago
Henry
▴ 10
0
votes
1
reply
311
views
plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
inna.gur
• 0
0
votes
1
reply
383
views
annotatePeak error for some problem
ChIPseeker
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
Jones
• 0
1
vote
2
replies
1.0k
views
how i can get the name of genes in pathway?
chipseq
ChIPseeker
14 months ago
chavaleab
• 0
0
votes
0
replies
570
views
Can ChiPseeker be as highly customizable as "computeMatrix"? for example if I want to plot the distribution of genes on the TAD boundary?
deeptools
ChIPseeker
14 months ago
840842906
• 0
0
votes
1
reply
822
views
Create an Annotation DB file for a non-model organism
AnnotationDbi
annotation
ChIPseeker
updated 15 months ago by
James W. MacDonald
65k • written 15 months ago by
L
▴ 50
0
votes
2
replies
3.2k
views
Cannot install packages in R/BiocManager_Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TR…
Bioconductor
BioCManager
ChIPseeker
updated 16 months ago by
James W. MacDonald
65k • written 16 months ago by
ASIF
• 0
1
vote
0
replies
646
views
Statistical test for genomic annotation by ChIPseeker
statistics
PeakAnnotation
ChIPseeker
GuangchuangYu
21 months ago
arisarkar88
▴ 40
0
votes
0
replies
792
views
Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene
ChIPseeker
annotate
22 months ago
Palmira
• 0
0
votes
0
replies
1.9k
views
How to define 'distal intergenic'
ChIPseeker
23 months ago
Sanghoon
• 0
0
votes
1
reply
970
views
ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
23 months ago
Gyan Prakash Mishra
▴ 10
0
votes
0
replies
692
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq
ChIPseeker
2.0 years ago
Swadha
• 0
0
votes
0
replies
710
views
What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
2.1 years ago
hyjforesight
• 0
0
votes
1
reply
1.6k
views
ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
2.5 years ago
william.ho
• 0
0
votes
2
replies
985
views
getPromoters
ChIPseeker
2.5 years ago
guoyou88
• 0
0
votes
0
replies
732
views
ChIPseeker, how to customize plotDistToTSS
ChIPseeker
2.6 years ago
alexandre.blais
▴ 50
1
vote
3
replies
894
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
2.9 years ago
Meghna
• 0
0
votes
0
replies
813
views
CHIPseeker- promoter gene names
ChIPseeker
CHIPsee
2.9 years ago
rb
• 0
0
votes
1
reply
1.4k
views
ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 3.1 years ago by
Sam
▴ 10 • written 3.1 years ago by
ikumar2000
▴ 10
0
votes
0
replies
839
views
What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
3.1 years ago
Sam
▴ 10
0
votes
0
replies
1.1k
views
Annotation of downstream in ChIPseeker
downstream
Priority
ChIPseeker
3.1 years ago
Xiaojie Cheng
• 0
0
votes
2
replies
1.0k
views
ChIPseeker failing on r-devel on CRAN checks
ChIPseeker
cinaR
3.1 years ago
Onur Karakaslar
• 0
1
vote
4
replies
2.0k
views
Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker
TxDb.Mmusculus.UCSC.mm10.knownGene
3.2 years ago
Kasit
• 0
0
votes
0
replies
688
views
ChIPSeeker covplot function, fix yaxis
ChIPseeker
3.3 years ago
jordi.planells
• 0
0
votes
0
replies
741
views
Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
3.4 years ago
Sam
▴ 10
2
votes
2
replies
2.4k
views
ChIP seeker annotation error
DiffBind
chipseq
ChIPseeker
ChipDb
annotation
3.5 years ago • updated 3.3 years ago
Mar Mar
▴ 20
5
votes
3
replies
1.3k
views
importing BED with non-integer values
ChIPseeker
ChIPSeqData
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
Morris
▴ 10
0
votes
0
replies
631
views
Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
3.5 years ago
Prasoon
• 0
0
votes
1
reply
1.4k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR
ChIPs
ChIPseeker
ChIPSeq
chipseq
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
ret28
• 0
0
votes
0
replies
894
views
About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
3.6 years ago
ahua217
▴ 10
0
votes
0
replies
768
views
How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
3.6 years ago
bioinfouser2
▴ 10
0
votes
1
reply
1.8k
views
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker
plotAnnoPie
3.7 years ago
amafon95
• 0
0
votes
1
reply
891
views
p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 9 months ago by
kyliecode
• 0 • written 3.8 years ago by
mwong043
• 0
0
votes
0
replies
861
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker
TxDb
getpromoters
software error
4.0 years ago
hfyuan2016
• 0
0
votes
0
replies
743
views
Potential oversimplification in the overlap function
ChIPseeker
4.0 years ago
konsta.kukkonen
• 0
1
vote
0
replies
879
views
Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
4.0 years ago
egbastakis
• 0
0
votes
1
reply
1.6k
views
ChIPSeeker with Ensembl IDs
chipseeker
Ensembl
EnsDb.Mmusculus.v79
ensembldb
4.1 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
1.0k
views
ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
4.2 years ago
Guandong Shang
▴ 40
0
votes
1
reply
1.6k
views
Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
4.6 years ago
sutturka
• 0
1
vote
2
replies
3.7k
views
Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq
ChIPseeker
peak annotation
annotatePeak()
Diffbind
4.6 years ago
researcher
• 0
2
votes
1
reply
3.6k
views
Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker
ChIPseeker
4.7 years ago
endrebak85
▴ 40
1
vote
3
replies
1.1k
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 4.8 years ago by
Martin Morgan
25k • written 4.8 years ago by
charlesgwellem
▴ 10
0
votes
1
reply
2.6k
views
error in readPeakFile {chipseeker}
ChIPseeker
readPeakFile
5.0 years ago
Theo
▴ 10
0
votes
1
reply
1.1k
views
Problem in using covplot ChIPseeker
ChIPseeker
software error
5.1 years ago
vasudha.sharma
• 0
3
votes
2
replies
1.7k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges
ChIPseeker
annotatePeak
TxDb
EnsDb
updated 5.2 years ago by
Johannes Rainer
★ 2.0k • written 5.2 years ago by
foehn
▴ 100
1
vote
1
reply
1.7k
views
ChIPseeker genomicAnnotationPriority
annotation
chipseeker
updated 2.8 years ago by
hqlkjx
• 0 • written 5.3 years ago by
dolata
▴ 10
0
votes
0
replies
1.1k
views
How to use ChIPseeker for getting genebody annotations.
chipseeker
chipseq
5.4 years ago
bioinfouser2
▴ 10
0
votes
2
replies
1.2k
views
how to get frequencies from plotDistToTSS
chipseeker
5.4 years ago
KKO
• 0
1
vote
0
replies
1.0k
views
ChipSeeker Flanking gene annotation
chipseeker
5.6 years ago
Lauma R
▴ 10
3
votes
4
replies
2.4k
views
ChIPseeker/Question about ''annoatePeak' function and for Bioconductor AnnotationData Packages for L.japonicus
chipseeker
Bioconductor AnnotationData Packages
Lotus japonicus
ChIPseq
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
egbastakis
• 0
50 results • Page
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Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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