Showing : ChIPseeker • reset
0
votes
0
replies
441
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
16 months ago Anton01 • 0
0
votes
0
replies
434
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
17 months ago Henry ▴ 10
0
votes
1
reply
689
views
plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 22 months ago by 68k • written 22 months ago by • 0
0
votes
2
replies
1.5k
views
annotatePeak error for some problem
ChIPseeker
written 22 months ago by • 0
1
vote
2
replies
1.7k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
2.5 years ago chavaleab • 0
0
votes
0
replies
982
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
2.5 years ago 840842906 • 0
0
votes
1
reply
1.5k
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 2.6 years ago by 68k • written 2.6 years ago by ▴ 50
0
votes
2
replies
6.4k
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 2.7 years ago by 68k • written 2.7 years ago by • 0
1
vote
0
replies
1.1k
views
Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
3.1 years ago arisarkar88 ▴ 40
0
votes
0
replies
1.3k
views
Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
3.2 years ago Palmira • 0
0
votes
0
replies
3.5k
views
How to define 'distal intergenic'
ChIPseeker
3.3 years ago Sanghoon • 0
0
votes
1
reply
1.6k
views
ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
3.3 years ago Gyan Prakash Mishra ▴ 10
0
votes
0
replies
1.0k
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
3.4 years ago Swadha • 0
0
votes
0
replies
1.1k
views
What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
3.5 years ago hyjforesight • 0
0
votes
1
reply
2.3k
views
ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
3.9 years ago william.ho • 0
0
votes
2
replies
1.5k
views
getPromoters
ChIPseeker
3.9 years ago guoyou88 • 0
0
votes
0
replies
1.1k
views
ChIPseeker, how to customize plotDistToTSS
ChIPseeker
4.0 years ago alexandre.blais ▴ 50
1
vote
3
replies
1.3k
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
4.2 years ago Meghna • 0
0
votes
0
replies
1.3k
views
CHIPseeker- promoter gene names
ChIPseeker CHIPsee
4.3 years ago rb • 0
0
votes
1
reply
2.1k
views
ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 4.4 years ago by ▴ 10 • written 4.4 years ago by ▴ 10
0
votes
0
replies
1.2k
views
What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
4.4 years ago Sam ▴ 10
0
votes
0
replies
1.5k
views
Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
4.5 years ago Xiaojie Cheng • 0
0
votes
2
replies
1.5k
views
ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
4.5 years ago Onur Karakaslar • 0
1
vote
4
replies
3.1k
views
Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
4.6 years ago Kasit • 0
0
votes
0
replies
1.0k
views
ChIPSeeker covplot function, fix yaxis
ChIPseeker
4.6 years ago jordi.planells • 0
0
votes
0
replies
1.0k
views
Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
4.8 years ago Sam ▴ 10
2
votes
2
replies
3.0k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
4.8 years ago • updated 4.6 years ago Mar Mar ▴ 20
5
votes
3
replies
2.8k
views
importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 4.8 years ago by 68k • written 4.8 years ago by ▴ 10
0
votes
0
replies
893
views
Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
4.9 years ago Prasoon • 0
0
votes
1
reply
2.2k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
0
votes
0
replies
1.3k
views
About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
4.9 years ago ahua217 ▴ 10
0
votes
0
replies
1.1k
views
How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
4.9 years ago bioinfouser2 ▴ 10
2
votes
1
reply
2.7k
views
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
5.0 years ago amafon95 ▴ 20
0
votes
1
reply
1.2k
views
p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 2.1 years ago by • 0 • written 5.1 years ago by • 0
0
votes
0
replies
1.3k
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
5.3 years ago hfyuan2016 • 0
0
votes
0
replies
1.1k
views
Potential oversimplification in the overlap function
ChIPseeker
5.3 years ago konsta.kukkonen • 0
1
vote
0
replies
1.2k
views
Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
5.4 years ago egbastakis • 0
0
votes
1
reply
2.1k
views
ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
5.4 years ago Assa Yeroslaviz ★ 1.5k
0
votes
1
reply
1.3k
views
ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
5.6 years ago Guandong Shang ▴ 40
0
votes
1
reply
2.1k
views
Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
6.0 years ago sutturka • 0
1
vote
2
replies
4.3k
views
Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
6.0 years ago researcher • 0
2
votes
1
reply
4.8k
views
Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
6.1 years ago endrebak85 ▴ 40
1
vote
3
replies
1.6k
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 6.2 years ago by 25k • written 6.2 years ago by ▴ 20
0
votes
1
reply
3.4k
views
error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
6.3 years ago Theo ▴ 10
0
votes
1
reply
1.5k
views
Problem in using covplot ChIPseeker
ChIPseeker software error
6.5 years ago vasudha.sharma • 0
3
votes
2
replies
2.4k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 6.6 years ago by ★ 2.1k • written 6.6 years ago by ▴ 100
1
vote
1
reply
2.2k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 4.1 years ago by • 0 • written 6.7 years ago by ▴ 10
0
votes
0
replies
1.5k
views
How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
6.7 years ago bioinfouser2 ▴ 10
0
votes
2
replies
1.5k
views
how to get frequencies from plotDistToTSS
chipseeker
6.8 years ago KKO • 0
1
vote
0
replies
1.4k
views
ChipSeeker Flanking gene annotation
chipseeker
7.0 years ago Lauma R ▴ 10
96 results • Page 1 of 2
Recent ...
Replies
Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Awards • All
Popular Question to rtrivedi1 ▴ 10
Popular Question to James W. MacDonald 68k
Popular Question to Assa Yeroslaviz ★ 1.5k
Popular Question to Nik dAK ▴ 10
Popular Question to Michael • 0
Locations • All
The city by the bay, 47 minutes ago
Spain, 2 hours ago
Pakistan, 2 hours ago
United Kingdom, 3 hours ago
united kingdom, 8 hours ago
Traffic: 694 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