Showing : AnnotationData • reset
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Annotation data packages for plant parasitic nematodes
AnnotationData Annotation
updated 19 months ago by 65k • written 19 months ago by • 0
0
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2
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5.1k
views
Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 20 months ago by ★ 1.6k • written 20 months ago by • 0
2
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10
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2.3k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 2.5 years ago by ★ 3.9k • written 2.5 years ago by • 0
3
votes
1
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2.2k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 2.6 years ago by 65k • written 2.6 years ago by • 0
2
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1
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1.4k
views
Retrieve gene description with ensembldb
biomaRt ensembldb AnnotationData
updated 3.1 years ago by ★ 2.0k • written 3.1 years ago by ▴ 510
4
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6
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1.2k
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 3.8 years ago by 65k • written 3.8 years ago by ▴ 10
2
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0
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985
views
News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 5.0 years ago by • 0 • written 5.0 years ago by 3.9k
0
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0
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980
views
News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
5.2 years ago shepherl 3.9k
1
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7
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1.1k
views
News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
5.6 years ago shepherl 3.9k
0
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0
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948
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News: ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit annotationdata News
5.8 years ago shepherl 3.9k
2
votes
1
reply
1.0k
views
How to get chip information from annotation databases
bioconductor annotationdata hgu133a
updated 6.1 years ago by 25k • written 6.1 years ago by ▴ 260
0
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3
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1.6k
views
Which annotationData package should I use?
annotationdata Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarray
updated 6.6 years ago by 65k • written 6.6 years ago by • 0
0
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3
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1.7k
views
Question about the ChIPpeakAnno:
ChIPchip Annotation AnnotationData ChIPchip Annotation AnnotationData
updated 6.9 years ago by • 0 • written 10.0 years ago by ★ 4.3k
1
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1
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1.2k
views
select function not working with annotation package; bug?
annotation annotationdata illuminaMousev1p1.db
updated 7.3 years ago by 65k • written 7.3 years ago by ★ 3.9k
3
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2
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1.5k
views
Trouble getting probe ID info from mouse4302.db annotation package with a specific RefSeq ID.
annotationdbi mouse4302 affymetrixchip annotationdata R
updated 8.5 years ago by 65k • written 8.5 years ago by • 0
1
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1
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1.2k
views
ChIPpeakAnno: Invalid row.names length in peaksNearBDP
Annotation AnnotationData Annotation AnnotationData
updated 9.7 years ago by ★ 4.3k • written 9.7 years ago by ▴ 30
0
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1
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1.7k
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ChIPpeakAnno: Maxgap option in annotatePeakInBatch
Lung AnnotationData ChIPpeakAnno Lung AnnotationData ChIPpeakAnno
9.7 years ago Julie Zhu ★ 4.3k
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3
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1.5k
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TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
10.8 years ago Alan Smith ▴ 150
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3
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1.8k
views
Use ChIPpeakAnno to find two-sided nearest genes to a peak
AnnotationData annotate ChIPpeakAnno AnnotationData annotate ChIPpeakAnno
11.4 years ago Julie Zhu ★ 4.3k
0
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1
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1.1k
views
Question about ChIPpeakAnno R package
AnnotationData annotate ChIPpeakAnno BayesPeak AnnotationData annotate ChIPpeakAnno
11.7 years ago Julie Zhu ★ 4.3k
0
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1
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983
views
ChIPpeakAnno
AnnotationData AnnotationData
updated 11.9 years ago by ★ 4.3k • written 11.9 years ago by ★ 13k
0
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4
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2.2k
views
ChIPpeakAnno as.data.frame error
GO AnnotationData annotate convert ChIPpeakAnno GO AnnotationData annotate convert
updated 12.2 years ago by ★ 4.3k • written 12.2 years ago by ▴ 910
0
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3
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1.1k
views
[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData AnnotationData
updated 12.5 years ago by ▴ 50 • written 12.5 years ago by ★ 4.3k
0
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0
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935
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[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData AnnotationData
12.5 years ago Halian Vilela ▴ 50
0
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1
reply
1.9k
views
Having trouble with new brainarray CDF
Microarray Annotation AnnotationData AffymetrixChip hgu133a2 cdf probe graph AnnotationDbi
updated 13.0 years ago by ★ 7.2k • written 13.0 years ago by ▴ 100
0
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0
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1.2k
views
Using ChIPpeakAnno on a non-mainstream organism
Transcription Annotation GO AnnotationData Organism BSgenome biomaRt BSgenome ChIPpeakAnno
13.0 years ago Julie Zhu ★ 4.3k
0
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1
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1.0k
views
[ENQUIRY] chIPpeakAnno annotatePeakInBatch
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
13.2 years ago Julie Zhu ★ 4.3k
0
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0
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1.0k
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Call for help about your Chippeakanno R package
Annotation Cancer AnnotationData ChIPpeakAnno Annotation Cancer AnnotationData ChIPpeakAnno
13.2 years ago Julie Zhu ★ 4.3k
0
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0
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1.1k
views
Gene Name annotation with ChIPpeakAnno
Annotation AnnotationData annotate convert biomaRt Annotation AnnotationData annotate
13.3 years ago Julie Zhu ★ 4.3k
0
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0
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984
views
ChIPpeakAnno bug?
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
13.5 years ago Julie Zhu ★ 4.3k
0
votes
7
replies
1.4k
views
ChIPpeakAnno annotatePeakInBatch error message
GO AnnotationData GO AnnotationData
14.0 years ago • updated 13.9 years ago Dario Strbenac ★ 1.5k
0
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3
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1.1k
views
ChIPpeakAnno Critical Bug
AnnotationData AnnotationData
updated 14.0 years ago by ★ 4.3k • written 14.0 years ago by ★ 1.5k
0
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0
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914
views
Chippeakanno, maxgap =1000
AnnotationData AnnotationData
14.0 years ago Julie Zhu ★ 4.3k
0
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0
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1.1k
views
ChIPpeakAnno Biomart Archive annotation querying
Annotation GO AnnotationData BSgenome biomaRt BSgenome ChIPpeakAnno Annotation GO biomaRt
14.4 years ago Khademul Islam ▴ 30
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1
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1.5k
views
ChIPpeakAnno Biomart annotation
Annotation GO AnnotationData BSgenome biomaRt BSgenome ChIPpeakAnno Annotation GO biomaRt
updated 14.4 years ago by ★ 4.3k • written 14.4 years ago by ▴ 30
35 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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