Showing : annotationdata • reset
0
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Annotation package for Manduca sexta
annotation Manducasexta AnnotationData
8 months ago GA ▴ 10
0
votes
4
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9.0k
views
Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 11 months ago by • 0 • written 3.3 years ago by • 0
0
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1
reply
953
views
Annotation data packages for plant parasitic nematodes
AnnotationData Annotation
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
2
votes
10
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3.6k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 4.1 years ago by ★ 4.1k • written 4.1 years ago by • 0
3
votes
1
reply
3.3k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
2
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1
reply
2.9k
views
Retrieve gene description with ensembldb
biomaRt ensembldb AnnotationData
updated 4.7 years ago by ★ 2.1k • written 4.7 years ago by ▴ 510
4
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6
replies
1.9k
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 10
2
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0
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1.4k
views
News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 6.6 years ago by • 0 • written 6.6 years ago by 4.2k
0
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0
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1.3k
views
News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
6.8 years ago shepherl 4.2k
1
vote
7
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1.5k
views
News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
7.1 years ago shepherl 4.2k
0
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0
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1.3k
views
News: ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit annotationdata News
7.4 years ago shepherl 4.2k
2
votes
1
reply
1.4k
views
How to get chip information from annotation databases
bioconductor annotationdata hgu133a
updated 7.7 years ago by 25k • written 7.7 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 8.2 years ago by 68k • written 8.2 years ago by • 0
0
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3
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2.2k
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Question about the ChIPpeakAnno:
ChIPchip Annotation AnnotationData ChIPchip Annotation AnnotationData
updated 8.5 years ago by • 0 • written 11.6 years ago by ★ 4.3k
1
vote
1
reply
1.5k
views
select function not working with annotation package; bug?
annotation annotationdata illuminaMousev1p1.db
updated 8.9 years ago by 68k • written 8.9 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 10.1 years ago by 68k • written 10.1 years ago by • 0
1
vote
1
reply
1.5k
views
ChIPpeakAnno: Invalid row.names length in peaksNearBDP
Annotation AnnotationData Annotation AnnotationData
updated 11.3 years ago by ★ 4.3k • written 11.3 years ago by ▴ 30
0
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1
reply
2.1k
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ChIPpeakAnno: Maxgap option in annotatePeakInBatch
Lung AnnotationData ChIPpeakAnno Lung AnnotationData ChIPpeakAnno
11.3 years ago Julie Zhu ★ 4.3k
0
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3
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1.9k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
12.4 years ago Alan Smith ▴ 150
0
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3
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2.3k
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Use ChIPpeakAnno to find two-sided nearest genes to a peak
AnnotationData annotate ChIPpeakAnno AnnotationData annotate ChIPpeakAnno
13.0 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
1.4k
views
Question about ChIPpeakAnno R package
AnnotationData annotate ChIPpeakAnno BayesPeak AnnotationData annotate ChIPpeakAnno
13.3 years ago Julie Zhu ★ 4.3k
0
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1
reply
1.3k
views
ChIPpeakAnno
AnnotationData AnnotationData
updated 13.5 years ago by ★ 4.3k • written 13.5 years ago by ★ 13k
0
votes
4
replies
2.7k
views
ChIPpeakAnno as.data.frame error
GO AnnotationData annotate convert ChIPpeakAnno GO AnnotationData annotate convert
updated 13.8 years ago by ★ 4.3k • written 13.8 years ago by ▴ 910
0
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3
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1.5k
views
[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData AnnotationData
updated 14.1 years ago by ▴ 50 • written 14.1 years ago by ★ 4.3k
0
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0
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1.2k
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[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData AnnotationData
14.1 years ago Halian Vilela ▴ 50
0
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1
reply
2.3k
views
Having trouble with new brainarray CDF
Microarray Annotation AnnotationData AffymetrixChip hgu133a2 cdf probe graph AnnotationDbi
updated 14.6 years ago by ★ 7.2k • written 14.6 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
14.6 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
14.8 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
14.8 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
14.9 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
1.2k
views
ChIPpeakAnno bug?
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
15.1 years ago Julie Zhu ★ 4.3k
0
votes
7
replies
1.9k
views
ChIPpeakAnno annotatePeakInBatch error message
GO AnnotationData GO AnnotationData
15.5 years ago Dario Strbenac ★ 1.6k
0
votes
3
replies
1.5k
views
ChIPpeakAnno Critical Bug
AnnotationData AnnotationData
updated 15.6 years ago by ★ 4.3k • written 15.6 years ago by ★ 1.6k
0
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0
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1.2k
views
Chippeakanno, maxgap =1000
AnnotationData AnnotationData
15.6 years ago Julie Zhu ★ 4.3k
0
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0
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1.4k
views
ChIPpeakAnno Biomart Archive annotation querying
Annotation GO AnnotationData BSgenome biomaRt BSgenome ChIPpeakAnno Annotation GO biomaRt
16.0 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 16.0 years ago by ★ 4.3k • written 16.0 years ago by ▴ 30
36 results • Page 1 of 1
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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