Showing : annotationdbi • reset
2
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4
replies
574
views
Annotation Dbi Error: unable to find an inherited method for function 'x' for signature "MaskedBSgenome"
BSgenome.Hsapiens.UCSC.hg19 AnnotationDbi
6 weeks ago Erica • 0
2
votes
3
replies
1.2k
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 3 months ago by 64k • written 18 months ago by • 0
0
votes
1
reply
322
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 7 months ago by 64k • written 7 months ago by • 0
0
votes
0
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339
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb AnnotationDbi Annotation
8 months ago • updated 7 months ago ahiser • 0
3
votes
3
replies
4.5k
views
failing to install the package org.Hs.eg.db in R (version 3.5.2 )
org.Hs.eg.db AnnotationDbi
updated 9 months ago by • 0 • written 4.8 years ago by • 0
0
votes
1
reply
524
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 9 months ago by 64k • written 9 months ago by ▴ 50
2
votes
3
replies
825
views
org.Hs.eg.db gives more than one ENTREZID for a gene symbol
org.Hs.eg.db AnnotationDbi
updated 10 months ago by 64k • written 10 months ago by • 0
0
votes
3
replies
562
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 10 months ago by 64k • written 10 months ago by • 0
0
votes
1
reply
524
views
Share Annotation Packages
OrgDb AnnotationDbi
updated 13 months ago by 3.6k • written 13 months ago by • 0
2
votes
3
replies
1.6k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 14 months ago by ▴ 100 • written 14 months ago by ▴ 10
0
votes
1
reply
920
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 15 months ago by 64k • written 15 months ago by • 0
0
votes
14
replies
4.3k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
6.8 years ago • updated 15 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
688
views
Bioconducter can not be installed on latest RStudio
AnnotationDbi biomaRt Bioconductor
updated 17 months ago by ★ 6.2k • written 17 months ago by • 0
2
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5
replies
1.3k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
19 months ago nhaus • 0
0
votes
1
reply
1.2k
views
Converting gene symbols to entrez ID
AnnotationDbi org.Mm.eg.db
updated 20 months ago by 64k • written 20 months ago by • 0
5
votes
11
replies
1.4k
views
Inconsistent data within org.Sc.sgd.db package
org.Sc.sgd.db AnnotationDbi
updated 21 months ago by • 0 • written 3.8 years ago by • 0
0
votes
2
replies
1.2k
views
AnnotationDbi
AnnotationDbi
2.1 years ago Bogdan ▴ 670
3
votes
1
reply
1.9k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 2.2 years ago by 64k • written 2.2 years ago by • 0
1
vote
6
replies
1.4k
views
what's the difference between this two AnnotationDbi::select type in GO select
GO.db AnnotationDbi
updated 2.2 years ago by • 0 • written 2.3 years ago by ▴ 40
0
votes
3
replies
868
views
Error using old ensembldb annotations with R 4.0 +
anno EnsDb.Hsapiens.v79 ensDb.HSapiens.v92 AnnotationDbi ensembldb
2.3 years ago rbenel ▴ 30
1
vote
2
replies
1.2k
views
Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db.
org.Mm.eg.db AnnotationDbi
updated 2.3 years ago by 64k • written 2.3 years ago by ▴ 30
1
vote
2
replies
938
views
What are these genes ? [How to get Ensembl IDs for them]
AnnotationDbi biomaRt
updated 2.3 years ago by ▴ 30 • written 2.3 years ago by • 0
3
votes
1
reply
965
views
[PrimeView] Affymetrix Human Gene Expression Array
AnnotationDbi [PrimeView]AffymetrixHumanGeneExpressionArray
updated 2.4 years ago by ★ 3.8k • written 2.4 years ago by • 0
1
vote
2
replies
2.2k
views
mapping mouse ENSEMBL ids to human gene symbol
Annotation AnnotationDbi annotate
updated 2.4 years ago by 64k • written 2.4 years ago by • 0
0
votes
1
reply
1.0k
views
failing to install the package org.Hs.eg.db in R (version 4.0.5 )
AnnotationDbi org.Hs.eg
updated 2.5 years ago by 64k • written 2.5 years ago by • 0
1
vote
2
replies
1.3k
views
trouble with ENSEMBL ids for Org.Ss.eg.db
Annotation org.Ss.eg.db AnnotationDbi
2.5 years ago carine.genet • 0
6
votes
6
replies
1.9k
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
2.5 years ago svlachavas ▴ 820
3
votes
3
replies
2.0k
views
Get the latest gene name from Entrez ID
AnnotationDbi org.Hs.eg.db
2.7 years ago sgupt46 • 0
1
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5
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1.1k
views
install Annotation Packages BSgenome.Osativa.MSU.MSU7 failed
Oryza_sativa AnnotationDbi
updated 2.7 years ago by 16k • written 2.7 years ago by • 0
0
votes
5
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929
views
annotaton hub will not load in R4.04 RStudio3.12
AnnotationDbi
written 2.7 years ago by • 0
3
votes
2
replies
2.0k
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi ensembldb
2.8 years ago Ezgi ▴ 60
13
votes
12
replies
5.4k
views
From a ENST to ENSG
AnnotationDbi
2.8 years ago suxxa ▴ 20
2
votes
3
replies
1.4k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 2.8 years ago by 64k • written 2.8 years ago by ▴ 20
3
votes
2
replies
1.6k
views
how to use select() to retrieve GO Biological Process Ancestors?
GO.db AnnotationDbi
updated 2.8 years ago by 25k • written 2.8 years ago by ★ 3.8k
4
votes
2
replies
1.2k
views
ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
AnnotationDbi EnsDb.Hsapiens org.Hs.eg.db
updated 2.9 years ago by ★ 2.0k • written 2.9 years ago by • 0
5
votes
7
replies
2.1k
views
Duplicated ENTREZID gene annotations org.Hs.eg.db
ENTREZID SYMBOL AnnotationDbi org.Hs.eg.db
updated 2.9 years ago by 48k • written 2.9 years ago by • 0
4
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4
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1.5k
views
Annotation with org.Hs.eg.db Genome Build 38
AnnotationDbi org.Hs.eg.db
3.0 years ago Bine ▴ 20
2
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3
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1.8k
views
Convert Refseq Protein IDs to UniProt IDs
AnnotationDbi
3.0 years ago sgupt46 • 0
4
votes
3
replies
1.8k
views
Gene conversion from SYMBOL to ENTREZ using AnnotationDbi doesn't convert some of the genes
AnnotationDbi org.Hs.eg.db
3.0 years ago Emilia ▴ 30
0
votes
7
replies
7.5k
views
AnnotationDbi Errors: unable to find an inherited method for function 'select' for signature 'character'.
AnnotationDbi
updated 3.3 years ago by 64k • written 3.3 years ago by • 0
0
votes
4
replies
1.3k
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 3.4 years ago by 64k • written 3.5 years ago by • 0
4
votes
5
replies
1.7k
views
makeOrgPackage - ERROR: Two fields in the source DB have the same name
software error AnnotationForge AnnotationDbi
updated 3.6 years ago by 64k • written 3.6 years ago by • 0
1
vote
5
replies
2.1k
views
Is org.Mm.eg.db updated to mus musculus version 99?
org.Mm.eg.db AnnotationDbi
3.6 years ago kavator ▴ 30
0
votes
1
reply
722
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 3.7 years ago by 25k • written 3.7 years ago by • 0
0
votes
4
replies
875
views
<N/A> Gene Ontology while using the AnnotationDbi package
go annotation annotationdbi
3.7 years ago CUCIO199 • 0
0
votes
2
replies
693
views
makeOrgPackage Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name
software error go AnnotationForge AnnotationDbi
updated 3.8 years ago by 64k • written 3.8 years ago by • 0
0
votes
3
replies
1.0k
views
None of the genes or compounds mapped to the pathway!
pathview AnnotationDbi
updated 4.2 years ago by 41k • written 4.2 years ago by • 0
2
votes
3
replies
1.7k
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport tximeta AnnotationDbi
4.4 years ago Benjamin • 0
1
vote
1
reply
932
views
The total genes items (e.g. ENTREZ ID, SYMBOL) in OrgDb (Salmo salar; [["AH66207"]]) is just half the gene number in NCBI ?!
Annotationhub Annotationdb profiler annotationdbi
4.6 years ago wecai • 0
4
votes
5
replies
1.3k
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 4.7 years ago by 64k • written 4.7 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: Obtaining rsIDs with ENSG and variant ID information by Robert Castelo ★ 3.0k
You should first and foremost find out what was the human reference genome version from which your dataset was derived. Assuming this was G…
Comment: DESeq2 - groups with biological replicates from the same patient by James W. MacDonald 64k
If by clustering you mean there might be a within-subject correlation, then yes it's a possibility. But you cannot control for that using a…
Comment: Why is DMRcate not available for Bioconductor version 3.18? by Mike Smith ★ 6.2k
If we hover over the tiny little red icon next to the Linux build report, we can see that the source package isn't being distributed becaus…
Comment: ClusterProfiler - enrichKEGG on specific pathways by EvaLan • 0
Hey bekah, I wonder if you have found the solution to solve this issue? Best wishes, EvaLan
Comment: Why is DMRcate not available for Bioconductor version 3.18? by Gordon Smyth 48k
That's a good question. On the DMRcate landing page, one can see that the "Source package" file is missing, meaning that installation in Un…
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Answer: limma::voom vs edgeR::voomLmFit - when to use?
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Answer: EdgeR: Exact test and glmQLFTest produce very different results
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