Showing : AnnotationData • reset
0
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6.5k
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Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 3 months ago by • 0 • written 2.1 years ago by • 0
0
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1
reply
722
views
Annotation data packages for plant parasitic nematodes
AnnotationData Annotation
updated 2.1 years ago by 67k • written 2.1 years ago by • 0
2
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10
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2.8k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 3.0 years ago by ★ 4.1k • written 3.0 years ago by • 0
3
votes
1
reply
2.5k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 3.1 years ago by 67k • written 3.1 years ago by • 0
2
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1
reply
1.9k
views
Retrieve gene description with ensembldb
biomaRt ensembldb AnnotationData
updated 3.5 years ago by ★ 2.1k • written 3.5 years ago by ▴ 510
4
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6
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1.4k
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 4.3 years ago by 67k • written 4.3 years ago by ▴ 10
2
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0
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1.1k
views
News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 5.4 years ago by • 0 • written 5.5 years ago by 4.0k
0
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0
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1.1k
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News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
5.7 years ago shepherl 4.0k
1
vote
7
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1.2k
views
News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
6.0 years ago shepherl 4.0k
0
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0
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1.1k
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News: ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit annotationdata News
6.2 years ago shepherl 4.0k
2
votes
1
reply
1.1k
views
How to get chip information from annotation databases
bioconductor annotationdata hgu133a
updated 6.6 years ago by 25k • written 6.6 years ago by ▴ 260
0
votes
3
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1.8k
views
Which annotationData package should I use?
annotationdata Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarray
updated 7.0 years ago by 67k • written 7.0 years ago by • 0
0
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3
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1.9k
views
Question about the ChIPpeakAnno:
ChIPchip Annotation AnnotationData ChIPchip Annotation AnnotationData
updated 7.4 years ago by • 0 • written 10.5 years ago by ★ 4.3k
1
vote
1
reply
1.3k
views
select function not working with annotation package; bug?
annotation annotationdata illuminaMousev1p1.db
updated 7.7 years ago by 67k • written 7.7 years ago by ★ 4.1k
3
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2
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1.6k
views
Trouble getting probe ID info from mouse4302.db annotation package with a specific RefSeq ID.
annotationdbi mouse4302 affymetrixchip annotationdata R
updated 8.9 years ago by 67k • written 8.9 years ago by • 0
1
vote
1
reply
1.3k
views
ChIPpeakAnno: Invalid row.names length in peaksNearBDP
Annotation AnnotationData Annotation AnnotationData
updated 10.1 years ago by ★ 4.3k • written 10.1 years ago by ▴ 30
0
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1
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1.8k
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ChIPpeakAnno: Maxgap option in annotatePeakInBatch
Lung AnnotationData ChIPpeakAnno Lung AnnotationData ChIPpeakAnno
10.2 years ago Julie Zhu ★ 4.3k
0
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3
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1.6k
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TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
11.2 years ago Alan Smith ▴ 150
0
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3
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2.0k
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Use ChIPpeakAnno to find two-sided nearest genes to a peak
AnnotationData annotate ChIPpeakAnno AnnotationData annotate ChIPpeakAnno
11.8 years ago Julie Zhu ★ 4.3k
0
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1
reply
1.2k
views
Question about ChIPpeakAnno R package
AnnotationData annotate ChIPpeakAnno BayesPeak AnnotationData annotate ChIPpeakAnno
12.2 years ago Julie Zhu ★ 4.3k
0
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1
reply
1.1k
views
ChIPpeakAnno
AnnotationData AnnotationData
updated 12.4 years ago by ★ 4.3k • written 12.4 years ago by ★ 13k
0
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4
replies
2.3k
views
ChIPpeakAnno as.data.frame error
GO AnnotationData annotate convert ChIPpeakAnno GO AnnotationData annotate convert
updated 12.6 years ago by ★ 4.3k • written 12.6 years ago by ▴ 910
0
votes
3
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1.2k
views
[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData AnnotationData
updated 12.9 years ago by ▴ 50 • written 12.9 years ago by ★ 4.3k
0
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0
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995
views
[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData AnnotationData
12.9 years ago Halian Vilela ▴ 50
0
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1
reply
2.0k
views
Having trouble with new brainarray CDF
Microarray Annotation AnnotationData AffymetrixChip hgu133a2 cdf probe graph AnnotationDbi
updated 13.4 years ago by ★ 7.2k • written 13.4 years ago by ▴ 100
0
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0
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1.3k
views
Using ChIPpeakAnno on a non-mainstream organism
Transcription Annotation GO AnnotationData Organism BSgenome biomaRt BSgenome ChIPpeakAnno
13.5 years ago Julie Zhu ★ 4.3k
0
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1
reply
1.1k
views
[ENQUIRY] chIPpeakAnno annotatePeakInBatch
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
13.6 years ago Julie Zhu ★ 4.3k
0
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0
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1.1k
views
Call for help about your Chippeakanno R package
Annotation Cancer AnnotationData ChIPpeakAnno Annotation Cancer AnnotationData ChIPpeakAnno
13.6 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
1.2k
views
Gene Name annotation with ChIPpeakAnno
Annotation AnnotationData annotate convert biomaRt Annotation AnnotationData annotate
13.7 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
1.1k
views
ChIPpeakAnno bug?
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
14.0 years ago Julie Zhu ★ 4.3k
0
votes
7
replies
1.6k
views
ChIPpeakAnno annotatePeakInBatch error message
GO AnnotationData GO AnnotationData
14.4 years ago Dario Strbenac ★ 1.5k
0
votes
3
replies
1.3k
views
ChIPpeakAnno Critical Bug
AnnotationData AnnotationData
updated 14.4 years ago by ★ 4.3k • written 14.4 years ago by ★ 1.5k
0
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0
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996
views
Chippeakanno, maxgap =1000
AnnotationData AnnotationData
14.4 years ago Julie Zhu ★ 4.3k
0
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0
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1.2k
views
ChIPpeakAnno Biomart Archive annotation querying
Annotation GO AnnotationData BSgenome biomaRt BSgenome ChIPpeakAnno Annotation GO biomaRt
14.9 years ago Khademul Islam ▴ 30
0
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1
reply
1.6k
views
ChIPpeakAnno Biomart annotation
Annotation GO AnnotationData BSgenome biomaRt BSgenome ChIPpeakAnno Annotation GO biomaRt
updated 14.9 years ago by ★ 4.3k • written 14.9 years ago by ▴ 30
35 results • Page 1 of 1
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Answer: Need help interpreting heatmaps from limma by James W. MacDonald 67k
Heatmaps don't do any comparisons. They just plot the underlying data in a matrix and color the blocks based (in your case) on the by-gene …
Comment: Are transformed values from rlog /vst log2 normalized counts? by Eva ▴ 10
I understood exactly what you said, but I got confused with the documentation and the info that gives about rlog because it seems to be tha…
Answer: featureCounts fails to load annotation file by James W. MacDonald 67k
I imagine Wei Shi will be along later with actual help, but for now do note that you can use an SAF file instead of a GTF. It's easy enough…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 67k
That error indicates that you have a file called NCBI.sqlite in your working directory that is missing some tables. You should delete that …
Comment: Are transformed values from rlog /vst log2 normalized counts? by James W. MacDonald 67k
The `DESeq2` package is meant to analyze count data! Most packages that are intended to be used for RNA-Seq data are going to want the raw …
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Answer: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Unable to install any Bioconductor package with new R 4.4.1 - path nor writable
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
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