Showing : ChiPseeker • reset
0
votes
0
replies
58
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
11 days ago Henry ▴ 10
0
votes
1
reply
303
views
plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 5 months ago by 65k • written 5 months ago by • 0
0
votes
1
reply
366
views
annotatePeak error for some problem
ChIPseeker
updated 5 months ago by 65k • written 5 months ago by • 0
1
vote
2
replies
1.0k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
13 months ago chavaleab • 0
0
votes
0
replies
565
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
13 months ago 840842906 • 0
0
votes
1
reply
808
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 14 months ago by 65k • written 14 months ago by ▴ 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 65k • written 16 months ago by • 0
1
vote
0
replies
629
views
Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
20 months ago arisarkar88 ▴ 40
0
votes
0
replies
780
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
22 months ago Sanghoon • 0
0
votes
1
reply
958
views
ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
23 months ago Gyan Prakash Mishra ▴ 10
0
votes
0
replies
686
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
24 months ago Swadha • 0
0
votes
0
replies
703
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
967
views
getPromoters
ChIPseeker
2.5 years ago guoyou88 • 0
0
votes
0
replies
725
views
ChIPseeker, how to customize plotDistToTSS
ChIPseeker
2.6 years ago alexandre.blais ▴ 50
1
vote
3
replies
883
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
2.8 years ago Meghna • 0
0
votes
0
replies
803
views
CHIPseeker- promoter gene names
ChIPseeker CHIPsee
2.9 years ago rb • 0
0
votes
1
reply
1.3k
views
ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 3.0 years ago by ▴ 10 • written 3.0 years ago by ▴ 10
0
votes
0
replies
825
views
What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
3.0 years ago Sam ▴ 10
0
votes
0
replies
1.0k
views
Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
3.1 years ago Xiaojie Cheng • 0
0
votes
2
replies
999
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
681
views
ChIPSeeker covplot function, fix yaxis
ChIPseeker
3.3 years ago jordi.planells • 0
0
votes
0
replies
732
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 3.2 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 65k • written 3.5 years ago by ▴ 10
0
votes
0
replies
622
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 65k • written 3.5 years ago by • 0
0
votes
0
replies
886
views
About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
3.5 years ago ahua217 ▴ 10
0
votes
0
replies
762
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
879
views
p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 8 months ago by • 0 • written 3.7 years ago by • 0
0
votes
0
replies
852
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
3.9 years ago hfyuan2016 • 0
0
votes
0
replies
735
views
Potential oversimplification in the overlap function
ChIPseeker
4.0 years ago konsta.kukkonen • 0
1
vote
0
replies
872
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
3.6k
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 25k • written 4.8 years ago by ▴ 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 ★ 2.0k • written 5.2 years ago by ▴ 100
1
vote
1
reply
1.7k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 2.8 years ago by • 0 • written 5.3 years ago by ▴ 10
0
votes
0
replies
1.1k
views
How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
5.3 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 65k • written 5.6 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Awards • All
Popular Question to shepherl 3.8k
Popular Question to James W. MacDonald 65k
Scholar to Michael Love 41k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Locations • All
France, 2 minutes ago
Canada, 3 minutes ago
Canada, 15 minutes ago
United States, 24 minutes ago
Ireland, 1 hour ago
Traffic: 938 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