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AnnotationData
•
reset
0
votes
7
replies
1.4k
views
ChIPpeakAnno annotatePeakInBatch error message
GO
AnnotationData
GO
AnnotationData
13.9 years ago
Dario Strbenac
★ 1.5k
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
2
replies
5.1k
views
Any tools to convert .gff to .gtf format
AnnotationData
CrispRdesignR
BSgenome
updated 20 months ago by
Malcolm Cook
★ 1.6k • written 20 months ago by
Manoj Kumar R
• 0
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
3
replies
1.7k
views
Question about the ChIPpeakAnno:
ChIPchip
Annotation
AnnotationData
ChIPchip
Annotation
AnnotationData
updated 6.9 years ago by
jinj
• 0 • written 10.0 years ago by
Julie Zhu
★ 4.3k
0
votes
3
replies
1.1k
views
ChIPpeakAnno Critical Bug
AnnotationData
AnnotationData
updated 14.0 years ago by
Julie Zhu
★ 4.3k • written 14.0 years ago by
Dario Strbenac
★ 1.5k
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
Julie Zhu
★ 4.3k • written 14.4 years ago by
Khademul Islam
▴ 30
0
votes
1
reply
592
views
Annotation data packages for plant parasitic nematodes
AnnotationData
Annotation
updated 19 months ago by
James W. MacDonald
65k • written 19 months ago by
Hassanaly
• 0
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
Julie Zhu
★ 4.3k • written 9.7 years ago by
Jens Preussner
▴ 30
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
James W. MacDonald
65k • written 8.4 years ago by
koreebay
• 0
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
James W. MacDonald
65k • written 7.2 years ago by
Guido Hooiveld
★ 3.9k
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
James W. MacDonald
65k • written 6.5 years ago by
peirinl
• 0
2
votes
1
reply
1.0k
views
How to get chip information from annotation databases
bioconductor
annotationdata
hgu133a
updated 6.1 years ago by
Martin Morgan
25k • written 6.1 years ago by
Agaz Hussain Wani
▴ 260
3
votes
6
replies
1.1k
views
Extremely big genes in annotation TxDb packages
annotation
txdb
AnnotationData
Genetics
updated 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
epibio
▴ 10
2
votes
1
reply
1.4k
views
Retrieve gene description with ensembldb
biomaRt
ensembldb
AnnotationData
updated 3.0 years ago by
Johannes Rainer
★ 2.0k • written 3.0 years ago by
António Miguel de Jesus Domingues
▴ 490
2
votes
10
replies
2.3k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter
annotationTools
AnnotationHub
AnnotationData
updated 2.5 years ago by
Guido Hooiveld
★ 3.9k • written 2.5 years ago by
Javan Okendo
• 0
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
James W. MacDonald
65k • written 2.6 years ago by
kstachelek
• 0
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
1.9k
views
Having trouble with new brainarray CDF
Microarray
Annotation
AnnotationData
AffymetrixChip
hgu133a2
cdf
probe
graph
AnnotationDbi
updated 13.0 years ago by
Marc Carlson
★ 7.2k • written 13.0 years ago by
Martha Behnke
▴ 100
0
votes
3
replies
1.1k
views
[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData
AnnotationData
updated 12.5 years ago by
Halian Vilela
▴ 50 • written 12.5 years ago by
Julie Zhu
★ 4.3k
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
Julie Zhu
★ 4.3k • written 12.1 years ago by
Mark Cowley
▴ 910
0
votes
1
reply
974
views
ChIPpeakAnno
AnnotationData
AnnotationData
updated 11.9 years ago by
Julie Zhu
★ 4.3k • written 11.9 years ago by
Guest User
★ 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
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
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
980
views
ChIPpeakAnno bug?
GO
AnnotationData
ChIPpeakAnno
GO
AnnotationData
ChIPpeakAnno
13.5 years ago
Julie Zhu
★ 4.3k
0
votes
0
replies
941
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
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
0
votes
0
replies
932
views
[ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?
AnnotationData
AnnotationData
12.5 years ago
Halian Vilela
▴ 50
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
977
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
nguyenlieuduoc
• 0 • written 5.0 years ago by
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
1.2k
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
908
views
Chippeakanno, maxgap =1000
AnnotationData
AnnotationData
14.0 years ago
Julie Zhu
★ 4.3k
35 results • Page
1 of 1
Recent ...
Replies
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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