Showing : AnnotationDbi • reset
2
votes
17
replies
985
views
Problem installing package, version of dependency issue
AnnotationDbi GO.db
updated 3 months ago by ▴ 730 • written 3 months ago by ▴ 50
2
votes
4
replies
919
views
Annotation Dbi Error: unable to find an inherited method for function 'x' for signature "MaskedBSgenome"
BSgenome.Hsapiens.UCSC.hg19 AnnotationDbi
6 months ago Erica • 0
2
votes
3
replies
1.6k
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 8 months ago by 65k • written 23 months ago by ▴ 30
0
votes
1
reply
527
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 12 months ago by 65k • written 12 months ago by • 0
0
votes
0
replies
504
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb AnnotationDbi Annotation
12 months ago ahiser • 0
3
votes
3
replies
5.0k
views
failing to install the package org.Hs.eg.db in R (version 3.5.2 )
org.Hs.eg.db AnnotationDbi
updated 14 months ago by • 0 • written 5.2 years ago by • 0
0
votes
1
reply
800
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 14 months ago by 65k • written 14 months ago by ▴ 50
2
votes
3
replies
1.2k
views
org.Hs.eg.db gives more than one ENTREZID for a gene symbol
org.Hs.eg.db AnnotationDbi
updated 15 months ago by 65k • written 15 months ago by • 0
0
votes
3
replies
734
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 15 months ago by 65k • written 15 months ago by • 0
0
votes
1
reply
672
views
Share Annotation Packages
OrgDb AnnotationDbi
updated 18 months ago by 3.8k • written 18 months ago by • 0
2
votes
3
replies
2.2k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 19 months ago by ▴ 120 • written 19 months ago by ▴ 10
0
votes
1
reply
1.1k
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
4.8k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
7.2 years ago • updated 20 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
874
views
Bioconducter can not be installed on latest RStudio
AnnotationDbi biomaRt Bioconductor
updated 22 months ago by ★ 6.5k • written 22 months ago by • 0
2
votes
5
replies
1.7k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
23 months 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 2.2 years ago by • 0 • written 4.2 years ago by • 0
0
votes
2
replies
1.4k
views
AnnotationDbi
AnnotationDbi
2.5 years ago Bogdan ▴ 670
3
votes
1
reply
2.1k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 2.6 years ago by 65k • written 2.6 years ago by • 0
1
vote
6
replies
1.8k
views
what's the difference between this two AnnotationDbi::select type in GO select
GO.db AnnotationDbi
updated 2.6 years ago by • 0 • written 2.6 years ago by ▴ 40
0
votes
3
replies
994
views
Error using old ensembldb annotations with R 4.0 +
anno EnsDb.Hsapiens.v79 ensDb.HSapiens.v92 AnnotationDbi ensembldb
2.7 years ago rbenel ▴ 40
1
vote
2
replies
1.4k
views
Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db.
org.Mm.eg.db AnnotationDbi
updated 2.7 years ago by 65k • written 2.7 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 2.7 years ago by ▴ 30 • written 2.7 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 ★ 3.9k • 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
2.9 years ago carine.genet • 0
6
votes
6
replies
2.2k
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
2.9 years ago svlachavas ▴ 830
3
votes
3
replies
2.4k
views
Get the latest gene name from Entrez ID
AnnotationDbi org.Hs.eg.db
3.1 years ago sgupt46 • 0
1
vote
5
replies
1.2k
views
install Annotation Packages BSgenome.Osativa.MSU.MSU7 failed
Oryza_sativa AnnotationDbi
updated 3.1 years ago by 16k • written 3.1 years ago by • 0
0
votes
5
replies
1.0k
views
annotaton hub will not load in R4.04 RStudio3.12
AnnotationDbi
written 3.1 years ago by • 0
3
votes
2
replies
2.4k
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi ensembldb
3.2 years ago Ezgi ▴ 60
13
votes
12
replies
6.5k
views
From a ENST to ENSG
AnnotationDbi
3.2 years ago suxxa ▴ 20
2
votes
3
replies
1.7k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 3.2 years ago by 65k • written 3.2 years ago by ▴ 30
3
votes
2
replies
1.9k
views
how to use select() to retrieve GO Biological Process Ancestors?
GO.db AnnotationDbi
updated 3.2 years ago by 25k • written 3.2 years ago by ★ 3.9k
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 3.3 years ago by • 0
5
votes
7
replies
2.5k
views
Duplicated ENTREZID gene annotations org.Hs.eg.db
ENTREZID SYMBOL AnnotationDbi org.Hs.eg.db
updated 3.3 years ago by 50k • written 3.3 years ago by • 0
4
votes
4
replies
1.9k
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
2.2k
views
Gene conversion from SYMBOL to ENTREZ using AnnotationDbi doesn't convert some of the genes
AnnotationDbi org.Hs.eg.db
3.4 years ago Emilia ▴ 30
0
votes
7
replies
8.4k
views
AnnotationDbi Errors: unable to find an inherited method for function 'select' for signature 'character'.
AnnotationDbi
updated 3.7 years ago by 65k • written 3.7 years ago by • 0
0
votes
4
replies
1.5k
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 3.8 years ago by 65k • written 3.8 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
4.0 years ago kavator ▴ 30
0
votes
1
reply
882
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
1.0k
views
<N/A> Gene Ontology while using the AnnotationDbi package
go annotation annotationdbi
4.1 years ago CUCIO199 • 0
0
votes
2
replies
793
views
makeOrgPackage Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name
software error go AnnotationForge AnnotationDbi
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
0
votes
3
replies
1.2k
views
None of the genes or compounds mapped to the pathway!
pathview AnnotationDbi
updated 4.6 years ago by 41k • written 4.6 years ago by • 0
2
votes
3
replies
2.0k
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport tximeta AnnotationDbi
4.8 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
5.0 years ago wecai • 0
50 results • Page 1 of 1
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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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