Showing : annotationdata • reset
2
votes
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
0
votes
7
replies
1.4k
views
ChIPpeakAnno annotatePeakInBatch error message
GO AnnotationData GO AnnotationData
13.9 years ago Dario Strbenac ★ 1.5k
1
vote
7
replies
1.1k
views
News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
5.5 years ago shepherl 3.8k
3
votes
6
replies
1.1k
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
0
votes
4
replies
2.2k
views
ChIPpeakAnno as.data.frame error
GO AnnotationData annotate convert ChIPpeakAnno GO AnnotationData annotate convert
updated 12.1 years ago by ★ 4.3k • written 12.1 years ago by ▴ 910
0
votes
3
replies
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
votes
3
replies
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
votes
3
replies
1.6k
views
Which annotationData package should I use?
annotationdata Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarray
updated 6.5 years ago by 65k • written 6.5 years ago by • 0
0
votes
3
replies
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
votes
3
replies
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
0
votes
3
replies
1.5k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
10.8 years ago Alan Smith ▴ 150
0
votes
2
replies
5.0k
views
Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 19 months ago by ★ 1.6k • written 20 months ago by • 0
3
votes
2
replies
1.5k
views
Trouble getting probe ID info from mouse4302.db annotation package with a specific RefSeq ID.
annotationdbi mouse4302 affymetrixchip annotationdata R
updated 8.4 years ago by 65k • written 8.4 years ago by • 0
0
votes
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
votes
1
reply
973
views
ChIPpeakAnno
AnnotationData AnnotationData
updated 11.9 years ago by ★ 4.3k • written 11.9 years ago by ★ 13k
0
votes
1
reply
1.1k
views
Question about ChIPpeakAnno R package
AnnotationData annotate ChIPpeakAnno BayesPeak AnnotationData annotate ChIPpeakAnno
11.7 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
1.0k
views
[ENQUIRY] chIPpeakAnno annotatePeakInBatch
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
13.1 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
1.7k
views
ChIPpeakAnno: Maxgap option in annotatePeakInBatch
Lung AnnotationData ChIPpeakAnno Lung AnnotationData ChIPpeakAnno
9.7 years ago Julie Zhu ★ 4.3k
1
vote
1
reply
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
1
vote
1
reply
1.2k
views
select function not working with annotation package; bug?
annotation annotationdata illuminaMousev1p1.db
updated 7.2 years ago by 65k • written 7.2 years ago by ★ 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
votes
1
reply
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
2
votes
1
reply
1.4k
views
Retrieve gene description with ensembldb
biomaRt ensembldb AnnotationData
updated 3.0 years ago by ★ 2.0k • written 3.0 years ago by ▴ 490
3
votes
1
reply
2.1k
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
0
votes
1
reply
591
views
Annotation data packages for plant parasitic nematodes
AnnotationData Annotation
updated 19 months ago by 65k • written 19 months ago by • 0
0
votes
0
replies
939
views
News: ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit annotationdata News
5.7 years ago shepherl 3.8k
0
votes
0
replies
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
0
votes
0
replies
1.0k
views
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
votes
0
replies
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
votes
0
replies
974
views
News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
5.2 years ago shepherl 3.8k
2
votes
0
replies
975
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 3.8k
0
votes
0
replies
980
views
ChIPpeakAnno bug?
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
13.5 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
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
votes
0
replies
907
views
Chippeakanno, maxgap =1000
AnnotationData AnnotationData
14.0 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
931
views
[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData AnnotationData
12.5 years ago Halian Vilela ▴ 50
35 results • Page 1 of 1
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Replies
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Dear Michael, I tried all three ways (the orIginal, increasing the number of required samples,and subsetting (the countdata and metadata be…
Comment: DESeq2 - dispersion estimation when there is none by Michael Love 41k
The red line does assume that shape but the fact the black points show that pattern is discussed in the 2014 paper. > Some caution is warr…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
I don't really follow what you are saying. All you have to do is delete the NCBI.sqlite db and *re-run the script exactly as you did above.…
Comment: Methylation Analysis experiment design using Limma by hortense96 • 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Comment: Limma design with continuous and categorical covariates by hortense96 • 0
Hello, I'm trying to do a differential methylation analysis with the Limma package and was wondering if you had any suggestions on how to …
Votes
Comment: DESeq2 - dispersion estimation when there is none
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
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