Showing : AnnotationData • reset
2
votes
10
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2.3k
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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 13.9 years ago by ★ 4.3k • written 13.9 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 12.4 years ago by ▴ 50 • written 12.4 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 19 months ago by • 0
3
votes
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 8.4 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
968
views
ChIPpeakAnno
AnnotationData AnnotationData
updated 11.9 years ago by ★ 4.3k • written 11.9 years ago by ★ 13k
0
votes
1
reply
1.0k
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 9.6 years ago by ★ 4.3k • written 9.7 years ago by ▴ 30
1
vote
1
reply
1.1k
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
1.4k
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
586
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
935
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
13.1 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
970
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
969
views
News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 4.9 years ago by • 0 • written 5.0 years ago by 3.8k
0
votes
0
replies
978
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
904
views
Chippeakanno, maxgap =1000
AnnotationData AnnotationData
14.0 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
928
views
[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData AnnotationData
12.4 years ago Halian Vilela ▴ 50
35 results • Page 1 of 1
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Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
As expected normalization is **way** off, meaning in simple terms that the cloud is too high. The deep-blue area should be along y=0. Try t…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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