Showing : Chipseeker • reset
0
votes
0
replies
281
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
7 months ago Anton01 • 0
0
votes
0
replies
249
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
8 months ago Henry ▴ 10
0
votes
1
reply
536
views
plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 13 months ago by 67k • written 13 months ago by • 0
0
votes
2
replies
966
views
annotatePeak error for some problem
ChIPseeker
written 13 months ago by • 0
1
vote
2
replies
1.4k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
21 months ago chavaleab • 0
0
votes
0
replies
768
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
21 months ago 840842906 • 0
0
votes
1
reply
1.2k
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 22 months ago by 67k • written 22 months ago by ▴ 50
0
votes
2
replies
5.0k
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 24 months ago by 67k • written 24 months ago by • 0
1
vote
0
replies
877
views
Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
2.4 years ago arisarkar88 ▴ 40
0
votes
0
replies
1.0k
views
Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
2.5 years ago Palmira • 0
0
votes
0
replies
2.8k
views
How to define 'distal intergenic'
ChIPseeker
2.5 years ago Sanghoon • 0
0
votes
1
reply
1.3k
views
ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
2.6 years ago Gyan Prakash Mishra ▴ 10
0
votes
0
replies
875
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
2.7 years ago Swadha • 0
0
votes
0
replies
927
views
What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
2.7 years ago hyjforesight • 0
0
votes
1
reply
2.0k
views
ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
3.1 years ago william.ho • 0
0
votes
2
replies
1.3k
views
getPromoters
ChIPseeker
3.2 years ago guoyou88 • 0
0
votes
0
replies
936
views
ChIPseeker, how to customize plotDistToTSS
ChIPseeker
3.2 years ago alexandre.blais ▴ 50
1
vote
3
replies
1.1k
views
what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
3.5 years ago Meghna • 0
0
votes
0
replies
1.0k
views
CHIPseeker- promoter gene names
ChIPseeker CHIPsee
3.6 years ago rb • 0
0
votes
1
reply
1.7k
views
ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 3.7 years ago by ▴ 10 • written 3.7 years ago by ▴ 10
0
votes
0
replies
1.0k
views
What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
3.7 years ago Sam ▴ 10
0
votes
0
replies
1.3k
views
Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
3.7 years ago Xiaojie Cheng • 0
0
votes
2
replies
1.2k
views
ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
3.8 years ago Onur Karakaslar • 0
1
vote
4
replies
2.6k
views
Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
3.8 years ago Kasit • 0
0
votes
0
replies
896
views
ChIPSeeker covplot function, fix yaxis
ChIPseeker
3.9 years ago jordi.planells • 0
0
votes
0
replies
899
views
Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
4.1 years ago Sam ▴ 10
2
votes
2
replies
2.8k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
4.1 years ago • updated 3.9 years ago Mar Mar ▴ 20
5
votes
3
replies
2.1k
views
importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 4.1 years ago by 67k • written 4.1 years ago by ▴ 10
0
votes
0
replies
752
views
Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
4.1 years ago Prasoon • 0
0
votes
1
reply
1.9k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 4.2 years ago by 67k • written 4.2 years ago by • 0
0
votes
0
replies
1.1k
views
About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
4.2 years ago ahua217 ▴ 10
0
votes
0
replies
910
views
How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
4.2 years ago bioinfouser2 ▴ 10
2
votes
1
reply
2.3k
views
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
4.3 years ago amafon95 ▴ 20
0
votes
1
reply
1.1k
views
p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 16 months ago by • 0 • written 4.4 years ago by • 0
0
votes
0
replies
1.1k
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
4.6 years ago hfyuan2016 • 0
0
votes
0
replies
949
views
Potential oversimplification in the overlap function
ChIPseeker
4.6 years ago konsta.kukkonen • 0
1
vote
0
replies
1.0k
views
Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
4.6 years ago egbastakis • 0
0
votes
1
reply
1.9k
views
ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
4.7 years ago Assa Yeroslaviz ★ 1.5k
0
votes
1
reply
1.2k
views
ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
4.8 years ago Guandong Shang ▴ 40
0
votes
1
reply
1.8k
views
Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
5.2 years ago sutturka • 0
1
vote
2
replies
4.0k
views
Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
5.3 years ago researcher • 0
2
votes
1
reply
4.3k
views
Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
5.3 years ago endrebak85 ▴ 40
1
vote
3
replies
1.4k
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 5.5 years ago by 25k • written 5.5 years ago by ▴ 10
0
votes
1
reply
3.1k
views
error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
5.6 years ago Theo ▴ 10
0
votes
1
reply
1.3k
views
Problem in using covplot ChIPseeker
ChIPseeker software error
5.8 years ago vasudha.sharma • 0
3
votes
2
replies
2.1k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 5.8 years ago by ★ 2.1k • written 5.9 years ago by ▴ 100
1
vote
1
reply
2.0k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 3.4 years ago by • 0 • written 6.0 years ago by ▴ 10
0
votes
0
replies
1.3k
views
How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
6.0 years ago bioinfouser2 ▴ 10
0
votes
2
replies
1.4k
views
how to get frequencies from plotDistToTSS
chipseeker
6.0 years ago KKO • 0
1
vote
0
replies
1.2k
views
ChipSeeker Flanking gene annotation
chipseeker
6.2 years ago Lauma R ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
Awards • All
Popular Question to Ali Barry ▴ 40
Popular Question to gabriel.hoffman ▴ 170
Popular Question to Jenny Drnevich ★ 2.0k
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
Locations • All
The city by the bay, 59 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
United Kingdom, 1 hour ago
United States, 2 hours ago
UPF, Barcelona, Spain, 4 hours ago
Traffic: 448 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