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ChiPseeker
•
reset
0
votes
0
replies
71
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
18 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
381
views
annotatePeak error for some problem
ChIPseeker
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
Jones
• 0
0
votes
1
reply
888
views
p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 9 months ago by
kyliecode
• 0 • written 3.8 years ago by
mwong043
• 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
819
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
645
views
Statistical test for genomic annotation by ChIPseeker
statistics
PeakAnnotation
ChIPseeker
GuangchuangYu
21 months ago
arisarkar88
▴ 40
0
votes
0
replies
791
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
984
views
getPromoters
ChIPseeker
2.5 years ago
guoyou88
• 0
0
votes
0
replies
730
views
ChIPseeker, how to customize plotDistToTSS
ChIPseeker
2.6 years ago
alexandre.blais
▴ 50
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
1
vote
3
replies
893
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
812
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 3.0 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
2
votes
2
replies
2.4k
views
ChIP seeker annotation error
DiffBind
chipseq
ChIPseeker
ChipDb
annotation
3.5 years ago • updated 3.2 years ago
Mar Mar
▴ 20
0
votes
0
replies
687
views
ChIPSeeker covplot function, fix yaxis
ChIPseeker
3.3 years ago
jordi.planells
• 0
0
votes
0
replies
740
views
Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
3.4 years ago
Sam
▴ 10
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
767
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
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
742
views
Potential oversimplification in the overlap function
ChIPseeker
4.0 years ago
konsta.kukkonen
• 0
1
vote
0
replies
878
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
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
1 of 1
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Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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