Showing : annotationdbi • reset
0
votes
3
replies
412
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
6 weeks ago Anna • 0
4
votes
7
replies
709
views
Mapping Between GenBank ID's and Uniprot
UniProt.ws AnnotationDbi
written 10 weeks ago by • 0
0
votes
0
replies
261
views
Improving Gene Matching for CIBERSORT Deconvolution with Monaco Reference Matrix in Bulk RNA-Seq
DeconRNASeq AnnotationDbi org.Hs.eg.db
11 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
693
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
911
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
813
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 4.3 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
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: Issue Installing Biostrings Package: gcc Compilation Errors by tiffanygrimmet • 0
@[tiny fishing](https://tiny-fishing.com) : You below have made too many mistakes in line 20, you have made quite a few mistakes in line 20…
Comment: How to use compareCluster in ClusterProfiler? by cynthiamoniz1122 • 0
@[poppy playtime chapter 3](https://poppyplaytimechapter3.io): Your code provides quite complete information, you code very detailed and sp…
Comment: Should tSNE from biol. replicates look alike? by cynthiamoniz1122 • 0
good ideal
Answer: Trying to convert ATACseq annotations of non-model species into human orthologs, by James W. MacDonald 67k
I would use the mapper I note above, and build your own `OrgDb`, then do the GO analysis directly. ``` > library(AnnotationForge) > option…
Comment: Trying to convert ATACseq annotations of non-model species into human orthologs, by James W. MacDonald 67k
There's already an `OrgDb` for this species on the AnnotationHub that hypothetically would be ideal, but there are almost no GO mappings, s…
Votes
Answer: Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
A: Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th
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