Showing : AnnotationData • reset
0
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3
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6.8k
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Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 5 months ago by • 0 • written 2.3 years ago by • 0
0
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1
reply
746
views
Annotation data packages for plant parasitic nematodes
AnnotationData Annotation
updated 2.2 years ago by 67k • written 2.2 years ago by • 0
2
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10
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2.9k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 3.1 years ago by ★ 4.1k • written 3.1 years ago by • 0
3
votes
1
reply
2.6k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 3.2 years ago by 67k • written 3.2 years ago by • 0
2
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1
reply
2.1k
views
Retrieve gene description with ensembldb
biomaRt ensembldb AnnotationData
updated 3.7 years ago by ★ 2.1k • written 3.7 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 4.4 years ago by 67k • written 4.4 years ago by ▴ 10
2
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0
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1.2k
views
News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 5.6 years ago by • 0 • written 5.6 years ago by 4.1k
0
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0
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1.1k
views
News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
5.8 years ago shepherl 4.1k
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
6.1 years ago shepherl 4.1k
0
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0
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1.1k
views
News: ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit annotationdata News
6.3 years ago shepherl 4.1k
2
votes
1
reply
1.2k
views
How to get chip information from annotation databases
bioconductor annotationdata hgu133a
updated 6.7 years ago by 25k • written 6.7 years ago by ▴ 260
0
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3
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1.9k
views
Which annotationData package should I use?
annotationdata Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarray
updated 7.2 years ago by 67k • written 7.2 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 7.5 years ago by • 0 • written 10.6 years ago by ★ 4.3k
1
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1
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1.3k
views
select function not working with annotation package; bug?
annotation annotationdata illuminaMousev1p1.db
updated 7.9 years ago by 67k • written 7.9 years ago by ★ 4.1k
3
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2
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1.7k
views
Trouble getting probe ID info from mouse4302.db annotation package with a specific RefSeq ID.
annotationdbi mouse4302 affymetrixchip annotationdata R
updated 9.0 years ago by 67k • written 9.0 years ago by • 0
1
vote
1
reply
1.4k
views
ChIPpeakAnno: Invalid row.names length in peaksNearBDP
Annotation AnnotationData Annotation AnnotationData
updated 10.3 years ago by ★ 4.3k • written 10.3 years ago by ▴ 30
0
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1
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1.9k
views
ChIPpeakAnno: Maxgap option in annotatePeakInBatch
Lung AnnotationData ChIPpeakAnno Lung AnnotationData ChIPpeakAnno
10.3 years ago Julie Zhu ★ 4.3k
0
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3
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1.6k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
11.4 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
12.0 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
12.3 years ago Julie Zhu ★ 4.3k
0
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1
reply
1.1k
views
ChIPpeakAnno
AnnotationData AnnotationData
updated 12.5 years ago by ★ 4.3k • written 12.5 years ago by ★ 13k
0
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4
replies
2.4k
views
ChIPpeakAnno as.data.frame error
GO AnnotationData annotate convert ChIPpeakAnno GO AnnotationData annotate convert
updated 12.8 years ago by ★ 4.3k • written 12.8 years ago by ▴ 910
0
votes
3
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1.3k
views
[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData AnnotationData
updated 13.1 years ago by ▴ 50 • written 13.1 years ago by ★ 4.3k
0
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0
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1.0k
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[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData AnnotationData
13.1 years ago Halian Vilela ▴ 50
0
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1
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2.0k
views
Having trouble with new brainarray CDF
Microarray Annotation AnnotationData AffymetrixChip hgu133a2 cdf probe graph AnnotationDbi
updated 13.6 years ago by ★ 7.2k • written 13.6 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
13.6 years ago Julie Zhu ★ 4.3k
0
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1
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1.2k
views
[ENQUIRY] chIPpeakAnno annotatePeakInBatch
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
13.7 years ago Julie Zhu ★ 4.3k
0
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0
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1.2k
views
Call for help about your Chippeakanno R package
Annotation Cancer AnnotationData ChIPpeakAnno Annotation Cancer AnnotationData ChIPpeakAnno
13.8 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
13.9 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
1.1k
views
ChIPpeakAnno bug?
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
14.1 years ago Julie Zhu ★ 4.3k
0
votes
7
replies
1.6k
views
ChIPpeakAnno annotatePeakInBatch error message
GO AnnotationData GO AnnotationData
14.5 years ago Dario Strbenac ★ 1.5k
0
votes
3
replies
1.3k
views
ChIPpeakAnno Critical Bug
AnnotationData AnnotationData
updated 14.6 years ago by ★ 4.3k • written 14.6 years ago by ★ 1.5k
0
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0
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1.0k
views
Chippeakanno, maxgap =1000
AnnotationData AnnotationData
14.6 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
15.0 years ago Khademul Islam ▴ 30
0
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1
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1.6k
views
ChIPpeakAnno Biomart annotation
Annotation GO AnnotationData BSgenome biomaRt BSgenome ChIPpeakAnno Annotation GO biomaRt
updated 15.0 years ago by ★ 4.3k • written 15.0 years ago by ▴ 30
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Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
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Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable by Gordon Smyth 52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
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That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0
> dim(spe) [1] 19962 425
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Answer: contrast matrix design for a continuous variable
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Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
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