Showing : annotationdbi • reset
0
votes
3
replies
412
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
6 weeks ago • updated 5 weeks ago Anna • 0
4
votes
7
replies
708
views
Mapping Between GenBank ID's and Uniprot
UniProt.ws AnnotationDbi
written 10 weeks ago by • 0
0
votes
0
replies
260
views
Improving Gene Matching for CIBERSORT Deconvolution with Monaco Reference Matrix in Bulk RNA-Seq
DeconRNASeq AnnotationDbi org.Hs.eg.db
10 weeks ago chunglee13 • 0
2
votes
17
replies
1.8k
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
11 months ago Erica • 0
0
votes
1
reply
665
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 17 months ago by 67k • written 17 months ago by • 0
0
votes
0
replies
692
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb AnnotationDbi Annotation
17 months ago ahiser • 0
0
votes
1
reply
1.0k
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 19 months ago by 67k • written 19 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
910
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 20 months ago by 67k • written 20 months ago by • 0
0
votes
1
reply
811
views
Share Annotation Packages
OrgDb AnnotationDbi
updated 23 months ago by 4.0k • written 23 months ago by • 0
2
votes
3
replies
2.7k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 24 months ago by ▴ 130 • written 24 months ago by ▴ 10
0
votes
1
reply
1.3k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 2.0 years ago by 67k • written 2.1 years ago by • 0
0
votes
1
reply
1.0k
views
Bioconducter can not be installed on latest RStudio
AnnotationDbi biomaRt Bioconductor
updated 2.2 years ago by ★ 6.5k • written 2.2 years ago by • 0
2
votes
3
replies
1.9k
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 13 months ago by 67k • written 2.3 years ago by ▴ 70
2
votes
5
replies
2.3k
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
2.9 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 3.0 years ago by 67k • written 3.0 years ago by • 0
1
vote
6
replies
2.2k
views
what's the difference between this two AnnotationDbi::select type in GO select
GO.db AnnotationDbi
updated 3.0 years ago by • 0 • written 3.0 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
3.1 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 3.1 years ago by 67k • written 3.1 years ago by ▴ 30
1
vote
2
replies
1.3k
views
What are these genes ? [How to get Ensembl IDs for them]
AnnotationDbi biomaRt
updated 3.1 years ago by ▴ 30 • written 3.1 years ago by • 0
3
votes
1
reply
1.4k
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
3.0k
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
1.7k
views
trouble with ENSEMBL ids for Org.Ss.eg.db
Annotation org.Ss.eg.db AnnotationDbi
3.3 years ago carine.genet • 0
6
votes
6
replies
2.6k
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
3.3 years ago svlachavas ▴ 830
5
votes
3
replies
2.9k
views
Get the latest gene name from Entrez ID
AnnotationDbi org.Hs.eg.db
3.5 years ago sgupt46 ▴ 10
0
votes
5
replies
1.2k
views
annotaton hub will not load in R4.04 RStudio3.12
AnnotationDbi
written 3.5 years ago by • 0
1
vote
5
replies
1.4k
views
install Annotation Packages BSgenome.Osativa.MSU.MSU7 failed
Oryza_sativa AnnotationDbi
updated 3.5 years ago by 16k • written 3.5 years ago by • 0
3
votes
2
replies
3.0k
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi ensembldb
3.6 years ago Ezgi ▴ 60
2
votes
3
replies
2.0k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 3.6 years ago by 67k • written 3.6 years ago by ▴ 30
13
votes
12
replies
7.5k
views
From a ENST to ENSG
AnnotationDbi
3.6 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 3.6 years ago by 25k • written 3.6 years ago by ★ 4.1k
4
votes
2
replies
1.6k
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 3.7 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 3.7 years ago by 51k • written 3.7 years ago by • 0
4
votes
4
replies
2.3k
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
3.8 years ago Emilia ▴ 40
0
votes
7
replies
9.1k
views
AnnotationDbi Errors: unable to find an inherited method for function 'select' for signature 'character'.
AnnotationDbi
updated 4.1 years ago by 67k • written 4.1 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 4.2 years ago by 67k • written 4.2 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
2.9k
views
Is org.Mm.eg.db updated to mus musculus version 99?
org.Mm.eg.db AnnotationDbi
4.4 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 2.6 years ago by • 0 • written 4.6 years ago by • 0
0
votes
2
replies
925
views
makeOrgPackage Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name
software error go AnnotationForge AnnotationDbi
updated 4.6 years ago by 67k • written 4.6 years ago by • 0
0
votes
3
replies
1.5k
views
None of the genes or compounds mapped to the pathway!
pathview AnnotationDbi
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
2
votes
3
replies
2.3k
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport tximeta AnnotationDbi
5.2 years ago Benjamin • 0
50 results • Page 1 of 1
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Comment: How to read OSCA book? by zr • 0
Got it, that had really confused me a bit, thank you for your help!
Comment: How to use removeBatchEffect for removing effect of multiple confounding variabl by James W. MacDonald 67k
Please don't add questions onto a four-year old post. Instead, start a new one. If you want to reference the old post, that's fine.
Answer: How to use removeBatchEffect for removing effect of multiple confounding variabl by bioinformata • 0
Is it feasible to remove batch effect with limma after variance stabilizing transformation of the gene expression , or is eough to use vst…
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by James W. MacDonald 67k
Hi Guido, It's that last filtering step. You are saying the NCBI Gene ID has to be unique AND the ontology has to be BP, which isn't what …
Comment: AffylmGUI does not start wit R 4.4.1 by richardallenfriedmanbrooklyn ▴ 20
Gordon, I found out what went wrong. The problem was that the xquartz distribution for mac from cran did not include tcltk! I found that b…
Votes
Answer: How to read OSCA book?
Answer: How to read OSCA book?
DESeq2 design and contrasts with 2 drug-treated and one control group
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
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