Showing : annotationdbi • reset
0
votes
1
reply
119
views
how do I convert an Ilumn IDREF to a CPG loci
AnnotationDbi Annotation annotation BiologicalQuestion
updated 7 days ago by 67k • written 8 days ago by • 0
2
votes
2
replies
138
views
SAS token for Annotation package
AnnotationDbi AnnotationForge
11 days ago KABILAN • 0
0
votes
3
replies
488
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
9 weeks ago Anna • 0
4
votes
7
replies
801
views
Mapping Between GenBank ID's and Uniprot
UniProt.ws AnnotationDbi
written 3 months ago by • 0
0
votes
0
replies
286
views
Improving Gene Matching for CIBERSORT Deconvolution with Monaco Reference Matrix in Bulk RNA-Seq
DeconRNASeq AnnotationDbi org.Hs.eg.db
3 months ago chunglee13 • 0
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
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
0
votes
1
reply
687
views
Mapping of probe IDs to gene gene symbols for Affymetrix Human Clariom D Assay platform
GeneMapping AnnotationDbi AffymetrixDataTestFiles GeneExpressionSignature org.Hs.eg.db
updated 18 months ago by 67k • written 18 months ago by • 0
0
votes
0
replies
726
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb AnnotationDbi Annotation
18 months ago ahiser • 0
0
votes
1
reply
1.1k
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 20 months ago by 67k • written 20 months ago by ▴ 50
2
votes
3
replies
1.7k
views
org.Hs.eg.db gives more than one ENTREZID for a gene symbol
org.Hs.eg.db AnnotationDbi
updated 20 months ago by 67k • written 20 months ago by • 0
0
votes
3
replies
933
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 21 months ago by 67k • written 21 months ago by • 0
0
votes
1
reply
836
views
Share Annotation Packages
OrgDb AnnotationDbi
updated 2.0 years ago by 4.0k • written 2.0 years ago by • 0
2
votes
3
replies
2.8k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 2.0 years ago by ▴ 130 • written 2.0 years ago by ▴ 10
0
votes
1
reply
1.4k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 2.1 years ago by 67k • written 2.1 years ago by • 0
0
votes
1
reply
1.1k
views
Bioconducter can not be installed on latest RStudio
AnnotationDbi biomaRt Bioconductor
updated 2.3 years ago by ★ 6.5k • written 2.3 years ago by • 0
2
votes
3
replies
2.0k
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 14 months ago by 67k • written 2.4 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
1
reply
1.7k
views
Converting gene symbols to entrez ID
AnnotationDbi org.Mm.eg.db
updated 2.5 years ago by 67k • written 2.5 years ago by • 0
0
votes
2
replies
1.8k
views
AnnotationDbi
AnnotationDbi
3.0 years ago Bogdan ▴ 670
3
votes
1
reply
2.5k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 3.1 years ago by 67k • written 3.1 years ago by • 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
0
votes
3
replies
1.2k
views
Error using old ensembldb annotations with R 4.0 +
anno EnsDb.Hsapiens.v79 ensDb.HSapiens.v92 AnnotationDbi ensembldb
3.2 years ago rbenel ▴ 40
1
vote
2
replies
1.7k
views
Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db.
org.Mm.eg.db AnnotationDbi
updated 3.2 years ago by 67k • written 3.2 years ago by ▴ 30
1
vote
2
replies
1.4k
views
What are these genes ? [How to get Ensembl IDs for them]
AnnotationDbi biomaRt
updated 3.2 years ago by ▴ 30 • written 3.2 years ago by • 0
3
votes
1
reply
1.5k
views
[PrimeView] Affymetrix Human Gene Expression Array
AnnotationDbi [PrimeView]AffymetrixHumanGeneExpressionArray
updated 3.2 years ago by ★ 4.1k • written 3.2 years ago by • 0
1
vote
2
replies
3.1k
views
mapping mouse ENSEMBL ids to human gene symbol
Annotation AnnotationDbi annotate
updated 3.2 years ago by 67k • written 3.2 years ago by • 0
0
votes
1
reply
1.3k
views
failing to install the package org.Hs.eg.db in R (version 4.0.5 )
AnnotationDbi org.Hs.eg
updated 3.3 years ago by 67k • written 3.3 years ago by • 0
1
vote
2
replies
1.8k
views
trouble with ENSEMBL ids for Org.Ss.eg.db
Annotation org.Ss.eg.db AnnotationDbi
3.4 years ago • updated 3.3 years ago carine.genet • 0
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
3
replies
3.0k
views
Get the latest gene name from Entrez ID
AnnotationDbi org.Hs.eg.db
3.6 years ago sgupt46 ▴ 10
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
3
votes
2
replies
3.1k
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi ensembldb
3.7 years ago Ezgi ▴ 60
2
votes
3
replies
2.0k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 3.7 years ago by 67k • written 3.7 years ago by ▴ 30
13
votes
12
replies
7.7k
views
From a ENST to ENSG
AnnotationDbi
3.7 years ago suxxa ▴ 20
3
votes
2
replies
2.3k
views
how to use select() to retrieve GO Biological Process Ancestors?
GO.db AnnotationDbi
updated 3.7 years ago by 25k • written 3.7 years ago by ★ 4.1k
4
votes
2
replies
1.7k
views
ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
AnnotationDbi EnsDb.Hsapiens org.Hs.eg.db
updated 3.7 years ago by ★ 2.1k • written 3.8 years 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
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
2
votes
3
replies
2.3k
views
Convert Refseq Protein IDs to UniProt IDs
AnnotationDbi
3.8 years ago sgupt46 ▴ 10
5
votes
3
replies
2.8k
views
Gene conversion from SYMBOL to ENTREZ using AnnotationDbi doesn't convert some of the genes
AnnotationDbi org.Hs.eg.db
3.9 years ago Emilia ▴ 40
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
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
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
0
votes
1
reply
1.0k
views
After "DBI" and "AnnotationDbi" are installed, the AnnotationDbi dependency package is still not available when "org.hs.eg.db" is installed
org.hs.eg.db AnnotationDbi
updated 4.5 years ago by 25k • written 4.5 years ago by • 0
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
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
0
votes
2
replies
942
views
makeOrgPackage Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name
software error go AnnotationForge AnnotationDbi
updated 4.7 years ago by 67k • written 4.7 years ago by • 0
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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