Showing : annotationdata • reset
2
votes
10
replies
752
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 7 months ago by ★ 3.2k • written 7 months ago by • 0
2
votes
1
reply
557
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 8 months ago by 59k • written 8 months ago by • 0
2
votes
1
reply
318
views
Retrieve gene description with ensembldb
biomaRt ensembldb AnnotationData
updated 13 months ago by ★ 1.9k • written 13 months ago by ▴ 480
3
votes
6
replies
464
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Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 23 months ago by 59k • written 23 months ago by ▴ 10
2
votes
0
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415
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News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 3.0 years ago by • 0 • written 3.1 years ago by 3.1k
0
votes
0
replies
485
views
News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
3.3 years ago shepherl 3.1k
1
vote
7
replies
587
views
News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
3.6 years ago shepherl 3.1k
0
votes
0
replies
521
views
News: ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit annotationdata News
3.8 years ago shepherl 3.1k
2
votes
1
reply
596
views
How to get chip information from annotation databases
bioconductor annotationdata hgu133a
updated 4.2 years ago by 25k • written 4.2 years ago by ▴ 260
0
votes
3
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1.0k
views
Which annotationData package should I use?
annotationdata Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarray
updated 4.6 years ago by 59k • written 4.6 years ago by • 0
0
votes
3
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1.1k
views
Question about the ChIPpeakAnno:
ChIPchip Annotation AnnotationData ChIPchip Annotation AnnotationData
updated 5.0 years ago by • 0 • written 8.1 years ago by ★ 4.3k
1
vote
1
reply
779
views
select function not working with annotation package; bug?
annotation annotationdata illuminaMousev1p1.db
updated 5.3 years ago by 59k • written 5.3 years ago by ★ 3.2k
3
votes
2
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1.1k
views
Trouble getting probe ID info from mouse4302.db annotation package with a specific RefSeq ID.
annotationdbi mouse4302 affymetrixchip annotationdata R
updated 6.5 years ago by 59k • written 6.5 years ago by • 0
1
vote
1
reply
846
views
ChIPpeakAnno: Invalid row.names length in peaksNearBDP
Annotation AnnotationData Annotation AnnotationData
updated 7.7 years ago by ★ 4.3k • written 7.7 years ago by ▴ 30
0
votes
1
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1.3k
views
ChIPpeakAnno: Maxgap option in annotatePeakInBatch
Lung AnnotationData ChIPpeakAnno Lung AnnotationData ChIPpeakAnno
7.8 years ago Julie Zhu ★ 4.3k
0
votes
3
replies
1.0k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
8.9 years ago Alan Smith ▴ 150
0
votes
3
replies
1.2k
views
Use ChIPpeakAnno to find two-sided nearest genes to a peak
AnnotationData annotate ChIPpeakAnno AnnotationData annotate ChIPpeakAnno
9.5 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
654
views
Question about ChIPpeakAnno R package
AnnotationData annotate ChIPpeakAnno BayesPeak AnnotationData annotate ChIPpeakAnno
9.8 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
625
views
ChIPpeakAnno
AnnotationData AnnotationData
updated 10.0 years ago by ★ 4.3k • written 10.0 years ago by ★ 12k
0
votes
4
replies
1.6k
views
ChIPpeakAnno as.data.frame error
GO AnnotationData annotate convert ChIPpeakAnno GO AnnotationData annotate convert
updated 10.2 years ago by ★ 4.3k • written 10.2 years ago by ▴ 910
0
votes
3
replies
731
views
[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData AnnotationData
updated 10.5 years ago by ▴ 50 • written 10.5 years ago by ★ 4.3k
0
votes
0
replies
634
views
[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData AnnotationData
10.5 years ago Halian Vilela ▴ 50
0
votes
1
reply
1.5k
views
Having trouble with new brainarray CDF
Microarray Annotation AnnotationData AffymetrixChip hgu133a2 cdf probe graph AnnotationDbi
updated 11.1 years ago by ★ 7.2k • written 11.1 years ago by ▴ 100
0
votes
0
replies
866
views
Using ChIPpeakAnno on a non-mainstream organism
Transcription Annotation GO AnnotationData Organism BSgenome biomaRt BSgenome ChIPpeakAnno
11.1 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
758
views
[ENQUIRY] chIPpeakAnno annotatePeakInBatch
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
11.2 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
692
views
Call for help about your Chippeakanno R package
Annotation Cancer AnnotationData ChIPpeakAnno Annotation Cancer AnnotationData ChIPpeakAnno
11.2 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
807
views
Gene Name annotation with ChIPpeakAnno
Annotation AnnotationData annotate convert biomaRt Annotation AnnotationData annotate
11.3 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
703
views
ChIPpeakAnno bug?
GO AnnotationData ChIPpeakAnno GO AnnotationData ChIPpeakAnno
11.6 years ago Julie Zhu ★ 4.3k
0
votes
7
replies
812
views
ChIPpeakAnno annotatePeakInBatch error message
GO AnnotationData GO AnnotationData
12.0 years ago Dario Strbenac ★ 1.5k
0
votes
3
replies
712
views
ChIPpeakAnno Critical Bug
AnnotationData AnnotationData
updated 12.0 years ago by ★ 4.3k • written 12.0 years ago by ★ 1.5k
0
votes
0
replies
587
views
Chippeakanno, maxgap =1000
AnnotationData AnnotationData
12.1 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
786
views
ChIPpeakAnno Biomart Archive annotation querying
Annotation GO AnnotationData BSgenome biomaRt BSgenome ChIPpeakAnno Annotation GO biomaRt
12.5 years ago Khademul Islam ▴ 30
0
votes
1
reply
1.1k
views
ChIPpeakAnno Biomart annotation
Annotation GO AnnotationData BSgenome biomaRt BSgenome ChIPpeakAnno Annotation GO biomaRt
updated 12.5 years ago by ★ 4.3k • written 12.5 years ago by ▴ 30
33 results • Page 1 of 1
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Comment: CPM after RUVseq by James W. MacDonald 59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq by James W. MacDonald 59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq by Jess • 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error by Laurent Gatto 1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue by shepherl 3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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