Showing : annotationdbi • reset
5
votes
22
replies
5.9k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 8.2 years ago by ★ 1.0k • written 9.7 years ago by • 0
3
votes
18
replies
3.1k
views
Annotating codelink data file
r codelink annotation annotationdbi
updated 9.5 years ago by ▴ 760 • written 9.5 years ago by ▴ 260
2
votes
17
replies
1.9k
views
Problem installing package, version of dependency issue
AnnotationDbi GO.db
updated 8 months ago by ▴ 750 • written 8 months ago by ▴ 50
0
votes
14
replies
5.3k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
7.7 years ago • updated 2.1 years ago Jenny Drnevich ★ 2.0k
8
votes
12
replies
4.2k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 7.1 years ago by ★ 2.1k • written 7.1 years ago by • 0
13
votes
12
replies
7.7k
views
From a ENST to ENSG
AnnotationDbi
3.7 years ago suxxa ▴ 20
5
votes
11
replies
1.8k
views
Inconsistent data within org.Sc.sgd.db package
org.Sc.sgd.db AnnotationDbi
updated 2.7 years ago by • 0 • written 4.7 years ago by • 0
7
votes
11
replies
6.6k
views
Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.probes
edgeR limma annotationhub kegga annotationdbi
updated 8.3 years ago by ▴ 20 • written 8.6 years ago by ▴ 20
5
votes
11
replies
1.9k
views
an error in BioMart regarding gene annotations
biomart AnnotationDbi
updated 6.3 years ago by ▴ 50 • written 6.3 years ago by ▴ 670
1
vote
9
replies
2.4k
views
AnnotationDbi: Select - Join order
AnnotationDbi
5.7 years ago faustfrankenstein • 0
4
votes
8
replies
4.9k
views
Annotating DEseq output using AnnotationDbi mapIds and most results say NA
AnnotationDbi mapIds org.Mm.eg.db ENSEMBLTRANS
updated 7.8 years ago by 67k • written 7.8 years ago by ▴ 10
1
vote
8
replies
2.1k
views
sqliteSendQuery in AnnotationDbi
annotationdbi
9.4 years ago jessica.hekman ▴ 40
4
votes
7
replies
801
views
Mapping Between GenBank ID's and Uniprot
UniProt.ws AnnotationDbi
written 3 months ago by • 0
5
votes
7
replies
3.0k
views
Duplicated ENTREZID gene annotations org.Hs.eg.db
ENTREZID SYMBOL AnnotationDbi org.Hs.eg.db
updated 3.8 years ago by 51k • written 3.8 years ago by • 0
0
votes
7
replies
9.3k
views
AnnotationDbi Errors: unable to find an inherited method for function 'select' for signature 'character'.
AnnotationDbi
updated 4.2 years ago by 67k • written 4.2 years ago by • 0
0
votes
7
replies
2.1k
views
ragene10st
Annotation GO Rattus norvegicus ChipName cdf probe affy AnnotationDbi AffyCompatible GO
updated 15.6 years ago by ▴ 630 • written 15.6 years ago by ▴ 370
0
votes
7
replies
1.9k
views
oligo and GenericPDInfo
affy oligoclasses oligo package pdinfobuilder annotationdbi
updated 7.2 years ago by 67k • written 7.2 years ago by ▴ 510
5
votes
7
replies
1.4k
views
Concatenation of Bimap
AnnotationDbi Concatenate
updated 8.9 years ago by 67k • written 8.9 years ago by ★ 1.5k
3
votes
6
replies
3.3k
views
Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
annotation ensembl annotationdbi
6.3 years ago vd4mmind • 0
1
vote
6
replies
2.3k
views
what's the difference between this two AnnotationDbi::select type in GO select
GO.db AnnotationDbi
updated 3.1 years ago by • 0 • written 3.1 years ago by ▴ 40
6
votes
6
replies
2.7k
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
3.4 years ago svlachavas ▴ 830
5
votes
6
replies
2.9k
views
Is mapId supposed to concatenate multiVals?
annotationdbi ensembldb
updated 7.4 years ago by ★ 2.1k • written 7.4 years ago by ★ 13k
0
votes
6
replies
2.4k
views
Missing as.list generic from AnnotationDbi?
annotate AnnotationDbi annotate AnnotationDbi
updated 10.1 years ago by ★ 2.0k • written 11.3 years ago by ★ 7.9k
19
votes
6
replies
38k
views
How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
rnaseq annotationdbi
updated 8.0 years ago by ★ 6.8k • written 8.1 years ago by ▴ 70
2
votes
5
replies
2.4k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
2.4 years ago nhaus ▴ 70
0
votes
5
replies
1.2k
views
annotaton hub will not load in R4.04 RStudio3.12
AnnotationDbi
written 3.6 years ago by • 0
1
vote
5
replies
1.4k
views
install Annotation Packages BSgenome.Osativa.MSU.MSU7 failed
Oryza_sativa AnnotationDbi
updated 3.6 years ago by 16k • written 3.6 years ago by • 0
2
votes
5
replies
1.7k
views
building a new annotation
Annotation AnnBuilder AnnotationDbi Annotation AnnBuilder AnnotationDbi
updated 15.6 years ago by ★ 7.2k • written 15.6 years ago by ▴ 10
0
votes
5
replies
1.5k
views
Wheat annotation
Annotation cdf AnnotationDbi Annotation cdf AnnotationDbi
updated 12.3 years ago by 67k • written 12.3 years ago by ★ 13k
0
votes
5
replies
2.2k
views
Error during makeOrgPackageFromNCBI
annotation annotationforge annotationdbi makeorgpackagefromncbi
9.7 years ago oliver.tills • 0
3
votes
5
replies
1.9k
views
Selecting few ids from reactome.db
annotationdbi reactome.db bug
updated 7.8 years ago by 25k • written 7.8 years ago by ▴ 750
3
votes
5
replies
1.9k
views
GO.db installation fails (MacOS, AnnotationDbi, R3.5.0)
GO bioclite R3.5 mac os x annotationdbi
updated 6.4 years ago by 25k • written 6.4 years ago by ▴ 30
4
votes
5
replies
1.7k
views
Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens.UCSC.hg19.knownGene
ensembl cdschrom org.Hs.eg.db AnnotationDbi SingleCellExperiment
updated 5.5 years ago by 67k • written 5.5 years ago by ▴ 10
4
votes
5
replies
2.1k
views
makeOrgPackage - ERROR: Two fields in the source DB have the same name
software error AnnotationForge AnnotationDbi
updated 4.4 years ago by 67k • written 4.4 years ago by • 0
1
vote
5
replies
3.0k
views
Is org.Mm.eg.db updated to mus musculus version 99?
org.Mm.eg.db AnnotationDbi
4.5 years ago kavator ▴ 30
3
votes
5
replies
3.2k
views
Map TxDb.Hsapiens.UCSC.hg19.knownGene TXID keys to ENSEMBL transcript ID or Refseq ID
annotationdbi
updated 7.8 years ago by 67k • written 7.8 years ago by ▴ 10
0
votes
5
replies
1.7k
views
problem with Category package and custom annotationDbi
Annotation Category AnnotationDbi Annotation Category AnnotationDbi
updated 16.0 years ago by ★ 5.5k • written 16.0 years ago by ▴ 830
0
votes
5
replies
1.7k
views
hyperGTest not working on custom annotation package
GOstats AnnotationDbi GO.db
updated 5.6 years ago by 67k • written 5.6 years ago by • 0
0
votes
4
replies
1.1k
views
AnnotationDBI
Annotation GO AnnotationDbi Annotation GO AnnotationDbi
updated 15.1 years ago by ★ 7.2k • written 15.1 years ago by ▴ 50
3
votes
4
replies
2.1k
views
DGE matrix annotation
DGE DESeq2 AnnotationDbi
updated 6.0 years ago by 67k • written 6.0 years ago by • 0
1
vote
4
replies
2.7k
views
biocLite updating problem with Ubuntu 17.10
ubuntu biocgenerics s4vectors IRanges annotationdbi
updated 6.8 years ago by 25k • written 6.8 years ago by • 0
2
votes
4
replies
1.3k
views
Annotation Dbi Error: unable to find an inherited method for function 'x' for signature "MaskedBSgenome"
BSgenome.Hsapiens.UCSC.hg19 AnnotationDbi
12 months ago Erica • 0
2
votes
4
replies
2.4k
views
Problems during the installation of AnnotationDbi and pasilla
AnnotationDbi
updated 10.0 years ago by ▴ 200 • written 10.0 years ago by • 0
4
votes
4
replies
2.4k
views
Annotation with org.Hs.eg.db Genome Build 38
AnnotationDbi org.Hs.eg.db
3.8 years ago Bine ▴ 50
0
votes
4
replies
1.8k
views
Wrong annotation (TSS/TTS) for many genes: keytype="GENEID" with mapIds(TxDb.Mmusculus.UCSC.mm10.knownGene)
AnnotationDbi annotation TxDb.Mmusculus.UCSC.mm10.knownGene
updated 4.3 years ago by 67k • written 4.3 years ago by • 0
0
votes
4
replies
2.4k
views
Installing beadarray
annotate geneplotter beadarray AnnotationDbi annotate geneplotter beadarray AnnotationDbi
updated 17.0 years ago by 21k • written 17.0 years ago by ▴ 270
0
votes
4
replies
1.2k
views
<N/A> Gene Ontology while using the AnnotationDbi package
go annotation annotationdbi
4.5 years ago CUCIO199 • 0
0
votes
4
replies
1.6k
views
Howto annotate blast subject.id with AnnotationDbi
Alignment GO annotate AnnotationDbi Alignment GO annotate AnnotationDbi
updated 11.4 years ago by ★ 7.2k • written 11.4 years ago by ▴ 40
0
votes
4
replies
3.1k
views
topGO annotations issue
topgo annotationdbi
9.7 years ago willmacnair • 0
0
votes
3
replies
1.1k
views
gcrma using deprecated package
probe matchprobes AnnotationDbi probe matchprobes AnnotationDbi
15.1 years ago Rullmann, J.A.C. Ton ▴ 40
50 results • Page 1 of 1
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Answer: How to subset voomLmFit (MArrayLM) object? by Gordon Smyth 51k
Yes, the current behaviour is absolutely intentional. It doesn't seem to me to be meaningful or useful to try to subset the EList object au…
Answer: Need help interpreting heatmaps from limma by James W. MacDonald 67k
Heatmaps don't do any comparisons. They just plot the underlying data in a matrix and color the blocks based (in your case) on the by-gene …
Comment: Are transformed values from rlog /vst log2 normalized counts? by Eva ▴ 10
I understood exactly what you said, but I got confused with the documentation and the info that gives about rlog because it seems to be tha…
Answer: featureCounts fails to load annotation file by James W. MacDonald 67k
I imagine Wei Shi will be along later with actual help, but for now do note that you can use an SAF file instead of a GTF. It's easy enough…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 67k
That error indicates that you have a file called NCBI.sqlite in your working directory that is missing some tables. You should delete that …
Votes
Answer: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Unable to install any Bioconductor package with new R 4.4.1 - path nor writable
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
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