Showing : annotationdbi • reset
2
votes
17
replies
1.1k
views
Problem installing package, version of dependency issue
AnnotationDbi GO.db
updated 4 months ago by ▴ 730 • written 4 months ago by ▴ 50
2
votes
4
replies
1000
views
Annotation Dbi Error: unable to find an inherited method for function 'x' for signature "MaskedBSgenome"
BSgenome.Hsapiens.UCSC.hg19 AnnotationDbi
7 months ago Erica • 0
2
votes
3
replies
1.6k
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 9 months ago by 65k • written 2.0 years ago by ▴ 30
0
votes
1
reply
548
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 13 months ago by 65k • written 13 months ago by • 0
0
votes
0
replies
545
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb AnnotationDbi Annotation
13 months ago ahiser • 0
3
votes
3
replies
5.1k
views
failing to install the package org.Hs.eg.db in R (version 3.5.2 )
org.Hs.eg.db AnnotationDbi
updated 15 months ago by • 0 • written 5.2 years ago by • 0
0
votes
1
reply
843
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 15 months ago by 65k • written 15 months ago by ▴ 50
2
votes
3
replies
1.3k
views
org.Hs.eg.db gives more than one ENTREZID for a gene symbol
org.Hs.eg.db AnnotationDbi
updated 16 months ago by 65k • written 16 months ago by • 0
0
votes
3
replies
762
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 16 months ago by 65k • written 16 months ago by • 0
0
votes
1
reply
694
views
Share Annotation Packages
OrgDb AnnotationDbi
updated 19 months ago by 3.9k • written 19 months ago by • 0
2
votes
3
replies
2.3k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 20 months ago by ▴ 120 • written 20 months ago by ▴ 10
0
votes
1
reply
1.2k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 20 months ago by 65k • written 20 months ago by • 0
0
votes
14
replies
4.9k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
7.3 years ago • updated 21 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
906
views
Bioconducter can not be installed on latest RStudio
AnnotationDbi biomaRt Bioconductor
updated 23 months ago by ★ 6.5k • written 23 months ago by • 0
2
votes
5
replies
1.8k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
2.0 years ago nhaus ▴ 30
0
votes
1
reply
1.5k
views
Converting gene symbols to entrez ID
AnnotationDbi org.Mm.eg.db
updated 2.1 years ago by 65k • written 2.1 years ago by • 0
5
votes
11
replies
1.6k
views
Inconsistent data within org.Sc.sgd.db package
org.Sc.sgd.db AnnotationDbi
updated 2.3 years ago by • 0 • written 4.3 years ago by • 0
0
votes
2
replies
1.5k
views
AnnotationDbi
AnnotationDbi
2.6 years ago Bogdan ▴ 670
3
votes
1
reply
2.2k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 2.7 years ago by 65k • written 2.7 years ago by • 0
1
vote
6
replies
1.9k
views
what's the difference between this two AnnotationDbi::select type in GO select
GO.db AnnotationDbi
updated 2.7 years ago by • 0 • written 2.7 years ago by ▴ 40
0
votes
3
replies
1.0k
views
Error using old ensembldb annotations with R 4.0 +
anno EnsDb.Hsapiens.v79 ensDb.HSapiens.v92 AnnotationDbi ensembldb
2.8 years ago rbenel ▴ 40
1
vote
2
replies
1.5k
views
Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db.
org.Mm.eg.db AnnotationDbi
updated 2.8 years ago by 65k • written 2.8 years ago by ▴ 30
1
vote
2
replies
1.1k
views
What are these genes ? [How to get Ensembl IDs for them]
AnnotationDbi biomaRt
updated 2.8 years ago by ▴ 30 • written 2.8 years ago by • 0
3
votes
1
reply
1.2k
views
[PrimeView] Affymetrix Human Gene Expression Array
AnnotationDbi [PrimeView]AffymetrixHumanGeneExpressionArray
updated 2.8 years ago by ★ 4.0k • written 2.8 years ago by • 0
1
vote
2
replies
2.6k
views
mapping mouse ENSEMBL ids to human gene symbol
Annotation AnnotationDbi annotate
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
votes
1
reply
1.2k
views
failing to install the package org.Hs.eg.db in R (version 4.0.5 )
AnnotationDbi org.Hs.eg
updated 2.9 years ago by 65k • written 2.9 years ago by • 0
1
vote
2
replies
1.5k
views
trouble with ENSEMBL ids for Org.Ss.eg.db
Annotation org.Ss.eg.db AnnotationDbi
3.0 years ago carine.genet • 0
6
votes
6
replies
2.3k
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
3.0 years ago svlachavas ▴ 830
3
votes
3
replies
2.5k
views
Get the latest gene name from Entrez ID
AnnotationDbi org.Hs.eg.db
3.2 years ago sgupt46 • 0
1
vote
5
replies
1.2k
views
install Annotation Packages BSgenome.Osativa.MSU.MSU7 failed
Oryza_sativa AnnotationDbi
updated 3.2 years ago by 16k • written 3.2 years ago by • 0
0
votes
5
replies
1.1k
views
annotaton hub will not load in R4.04 RStudio3.12
AnnotationDbi
written 3.2 years ago by • 0
3
votes
2
replies
2.6k
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi ensembldb
3.3 years ago Ezgi ▴ 60
13
votes
12
replies
6.7k
views
From a ENST to ENSG
AnnotationDbi
3.3 years ago suxxa ▴ 20
2
votes
3
replies
1.7k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 3.3 years ago by 65k • written 3.3 years ago by ▴ 30
3
votes
2
replies
2.0k
views
how to use select() to retrieve GO Biological Process Ancestors?
GO.db AnnotationDbi
updated 3.3 years ago by 25k • written 3.3 years ago by ★ 4.0k
4
votes
2
replies
1.4k
views
ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
AnnotationDbi EnsDb.Hsapiens org.Hs.eg.db
updated 3.3 years ago by ★ 2.0k • written 3.4 years ago by • 0
5
votes
7
replies
2.6k
views
Duplicated ENTREZID gene annotations org.Hs.eg.db
ENTREZID SYMBOL AnnotationDbi org.Hs.eg.db
updated 3.4 years ago by 50k • written 3.4 years ago by • 0
4
votes
4
replies
2.0k
views
Annotation with org.Hs.eg.db Genome Build 38
AnnotationDbi org.Hs.eg.db
3.4 years ago Bine ▴ 40
2
votes
3
replies
2.0k
views
Convert Refseq Protein IDs to UniProt IDs
AnnotationDbi
3.4 years ago sgupt46 • 0
4
votes
3
replies
2.3k
views
Gene conversion from SYMBOL to ENTREZ using AnnotationDbi doesn't convert some of the genes
AnnotationDbi org.Hs.eg.db
3.5 years ago Emilia ▴ 30
0
votes
7
replies
8.5k
views
AnnotationDbi Errors: unable to find an inherited method for function 'select' for signature 'character'.
AnnotationDbi
updated 3.8 years ago by 65k • written 3.8 years ago by • 0
0
votes
4
replies
1.6k
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 3.9 years ago by 65k • written 3.9 years ago by • 0
4
votes
5
replies
1.9k
views
makeOrgPackage - ERROR: Two fields in the source DB have the same name
software error AnnotationForge AnnotationDbi
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
1
vote
5
replies
2.5k
views
Is org.Mm.eg.db updated to mus musculus version 99?
org.Mm.eg.db AnnotationDbi
4.1 years ago kavator ▴ 30
0
votes
1
reply
908
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 4.1 years ago by 25k • written 4.1 years ago by • 0
0
votes
4
replies
1.1k
views
<N/A> Gene Ontology while using the AnnotationDbi package
go annotation annotationdbi
4.1 years ago CUCIO199 • 0
0
votes
2
replies
815
views
makeOrgPackage Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name
software error go AnnotationForge AnnotationDbi
updated 4.3 years ago by 65k • written 4.3 years ago by • 0
0
votes
3
replies
1.3k
views
None of the genes or compounds mapped to the pathway!
pathview AnnotationDbi
updated 4.7 years ago by 42k • written 4.7 years ago by • 0
2
votes
3
replies
2.0k
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport tximeta AnnotationDbi
4.9 years ago Benjamin • 0
1
vote
1
reply
1.1k
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
5.1 years ago wecai • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 65k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 65k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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