Showing : AnnotationData • reset
0
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551
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Annotation package for Manduca sexta
annotation Manducasexta AnnotationData
5 months ago GA ▴ 10
0
votes
4
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8.7k
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Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 8 months ago by • 0 • written 3.0 years ago by • 0
0
votes
1
reply
897
views
Annotation data packages for plant parasitic nematodes
AnnotationData Annotation
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
2
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10
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3.4k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 3.9 years ago by ★ 4.1k • written 3.9 years ago by • 0
3
votes
1
reply
3.1k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
2
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1
reply
2.8k
views
Retrieve gene description with ensembldb
biomaRt ensembldb AnnotationData
updated 4.4 years ago by ★ 2.1k • written 4.4 years ago by ▴ 510
4
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6
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1.8k
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 5.2 years ago by 68k • written 5.2 years ago by ▴ 10
2
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0
replies
1.3k
views
News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 6.3 years ago by • 0 • written 6.4 years ago by 4.2k
0
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0
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1.3k
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News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
6.6 years ago shepherl 4.2k
1
vote
7
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1.4k
views
News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
6.9 years ago shepherl 4.2k
0
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0
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1.2k
views
News: ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit annotationdata News
7.1 years ago shepherl 4.2k
2
votes
1
reply
1.3k
views
How to get chip information from annotation databases
bioconductor annotationdata hgu133a
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 260
0
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3
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2.1k
views
Which annotationData package should I use?
annotationdata Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarray
updated 7.9 years ago by 68k • written 7.9 years ago by • 0
0
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3
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2.1k
views
Question about the ChIPpeakAnno:
ChIPchip Annotation AnnotationData ChIPchip Annotation AnnotationData
updated 8.3 years ago by • 0 • written 11.4 years ago by ★ 4.3k
1
vote
1
reply
1.4k
views
select function not working with annotation package; bug?
annotation annotationdata illuminaMousev1p1.db
updated 8.6 years ago by 68k • written 8.6 years ago by ★ 4.1k
3
votes
2
replies
1.9k
views
Trouble getting probe ID info from mouse4302.db annotation package with a specific RefSeq ID.
annotationdbi mouse4302 affymetrixchip annotationdata R
updated 9.8 years ago by 68k • written 9.8 years ago by • 0
1
vote
1
reply
1.5k
views
ChIPpeakAnno: Invalid row.names length in peaksNearBDP
Annotation AnnotationData Annotation AnnotationData
updated 11.0 years ago by ★ 4.3k • written 11.0 years ago by ▴ 30
0
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1
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2.0k
views
ChIPpeakAnno: Maxgap option in annotatePeakInBatch
Lung AnnotationData ChIPpeakAnno Lung AnnotationData ChIPpeakAnno
11.1 years ago Julie Zhu ★ 4.3k
0
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3
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1.8k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
12.2 years ago Alan Smith ▴ 150
0
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3
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2.2k
views
Use ChIPpeakAnno to find two-sided nearest genes to a peak
AnnotationData annotate ChIPpeakAnno AnnotationData annotate ChIPpeakAnno
12.8 years ago Julie Zhu ★ 4.3k
0
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1
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1.4k
views
Question about ChIPpeakAnno R package
AnnotationData annotate ChIPpeakAnno BayesPeak AnnotationData annotate ChIPpeakAnno
13.1 years ago Julie Zhu ★ 4.3k
0
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1
reply
1.2k
views
ChIPpeakAnno
AnnotationData AnnotationData
updated 13.3 years ago by ★ 4.3k • written 13.3 years ago by ★ 13k
0
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4
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2.6k
views
ChIPpeakAnno as.data.frame error
GO AnnotationData annotate convert ChIPpeakAnno GO AnnotationData annotate convert
updated 13.5 years ago by ★ 4.3k • written 13.5 years ago by ▴ 910
0
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3
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1.4k
views
[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData AnnotationData
updated 13.8 years ago by ▴ 50 • written 13.8 years ago by ★ 4.3k
0
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0
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1.1k
views
[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData AnnotationData
13.8 years ago Halian Vilela ▴ 50
0
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1
reply
2.2k
views
Having trouble with new brainarray CDF
Microarray Annotation AnnotationData AffymetrixChip hgu133a2 cdf probe graph AnnotationDbi
updated 14.4 years ago by ★ 7.2k • written 14.4 years ago by ▴ 100
0
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0
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1.5k
views
Using ChIPpeakAnno on a non-mainstream organism
Transcription Annotation GO AnnotationData Organism BSgenome biomaRt BSgenome ChIPpeakAnno
14.4 years ago Julie Zhu ★ 4.3k
0
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1
reply
1.3k
views
[ENQUIRY] chIPpeakAnno annotatePeakInBatch
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
14.5 years ago Julie Zhu ★ 4.3k
0
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0
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1.3k
views
Call for help about your Chippeakanno R package
Annotation Cancer AnnotationData ChIPpeakAnno Annotation Cancer AnnotationData ChIPpeakAnno
14.5 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
1.3k
views
Gene Name annotation with ChIPpeakAnno
Annotation AnnotationData annotate convert biomaRt Annotation AnnotationData annotate
14.6 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
1.2k
views
ChIPpeakAnno bug?
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
14.9 years ago Julie Zhu ★ 4.3k
0
votes
7
replies
1.9k
views
ChIPpeakAnno annotatePeakInBatch error message
GO AnnotationData GO AnnotationData
15.3 years ago Dario Strbenac ★ 1.6k
0
votes
3
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1.5k
views
ChIPpeakAnno Critical Bug
AnnotationData AnnotationData
updated 15.3 years ago by ★ 4.3k • written 15.3 years ago by ★ 1.6k
0
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0
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1.1k
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Chippeakanno, maxgap =1000
AnnotationData AnnotationData
15.4 years ago Julie Zhu ★ 4.3k
0
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0
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1.3k
views
ChIPpeakAnno Biomart Archive annotation querying
Annotation GO AnnotationData BSgenome biomaRt BSgenome ChIPpeakAnno Annotation GO biomaRt
15.8 years ago Khademul Islam ▴ 30
0
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1
reply
1.8k
views
ChIPpeakAnno Biomart annotation
Annotation GO AnnotationData BSgenome biomaRt BSgenome ChIPpeakAnno Annotation GO biomaRt
updated 15.8 years ago by ★ 4.3k • written 15.8 years ago by ▴ 30
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Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …
Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k
> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…
Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
Comment: voomLmFit fitted log-CPM values by Lina ▴ 10
Is the output from fitted(v) in the log2 CPM scale? or CPM scale?
Answer: voomLmFit fitted log-CPM values by Gordon Smyth 53k
Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```
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A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
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