Showing : annotationdbi • reset
3
votes
9
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1.5k
views
Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) returning drastically different numbers of transcripts
AnnotationDbi EnsDb.Mmusculus.v79 biomaRt org.Mm.eg.db
updated 5 months ago by • 0 • written 6 months ago by • 0
2
votes
3
replies
1.5k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 7 months ago by 68k • written 7 months ago by ▴ 10
0
votes
2
replies
898
views
GOstats kegg analysis in wheat - help - none of the objects in the first column are legitimate kegg ids (but they are)
AnnotationDbi GOstats
8 months ago GV Yoshikawa • 0
5
votes
13
replies
2.2k
views
Installing annotation package in locally
AnnotationDbi AnnotationHub Annotation AnnotationForge
8 months ago KABILAN • 0
0
votes
1
reply
423
views
how do I convert an Ilumn IDREF to a CPG loci
AnnotationDbi Annotation annotation BiologicalQuestion
updated 9 months ago by 68k • written 9 months ago by • 0
2
votes
2
replies
437
views
SAS token for Annotation package
AnnotationDbi AnnotationForge
9 months ago KABILAN • 0
0
votes
3
replies
1.3k
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
11 months ago Anna • 0
5
votes
7
replies
2.6k
views
Mapping Between GenBank ID's and Uniprot
UniProt.ws AnnotationDbi
written 12 months ago by • 0
0
votes
0
replies
584
views
Improving Gene Matching for CIBERSORT Deconvolution with Monaco Reference Matrix in Bulk RNA-Seq
DeconRNASeq AnnotationDbi org.Hs.eg.db
12 months ago chunglee13 • 0
2
votes
17
replies
3.7k
views
Problem installing package, version of dependency issue
AnnotationDbi GO.db
updated 17 months ago by ▴ 760 • written 17 months ago by ▴ 50
2
votes
4
replies
2.2k
views
Annotation Dbi Error: unable to find an inherited method for function 'x' for signature "MaskedBSgenome"
BSgenome.Hsapiens.UCSC.hg19 AnnotationDbi
21 months ago Erica • 0
0
votes
1
reply
987
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 2.2 years ago by 68k • written 2.3 years ago by • 0
0
votes
0
replies
971
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb AnnotationDbi Annotation
2.3 years ago ahiser • 0
0
votes
1
reply
1.4k
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 50
2
votes
3
replies
2.4k
views
org.Hs.eg.db gives more than one ENTREZID for a gene symbol
org.Hs.eg.db AnnotationDbi
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
votes
3
replies
1.2k
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
votes
1
reply
983
views
Share Annotation Packages
OrgDb AnnotationDbi
updated 2.7 years ago by 4.2k • written 2.7 years ago by • 0
2
votes
3
replies
3.7k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 2.8 years ago by ▴ 150 • written 2.8 years ago by ▴ 10
0
votes
1
reply
1.7k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
votes
1
reply
1.4k
views
Bioconducter can not be installed on latest RStudio
AnnotationDbi biomaRt Bioconductor
updated 3.0 years ago by ★ 6.6k • written 3.0 years ago by • 0
2
votes
3
replies
2.5k
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 23 months ago by 68k • written 3.1 years ago by ▴ 70
2
votes
5
replies
3.5k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
3.2 years ago nhaus ▴ 70
0
votes
1
reply
2.1k
views
Converting gene symbols to entrez ID
AnnotationDbi org.Mm.eg.db
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
0
votes
2
replies
2.3k
views
AnnotationDbi
AnnotationDbi
3.7 years ago Bogdan ▴ 670
3
votes
1
reply
3.0k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
1
vote
6
replies
2.9k
views
what's the difference between this two AnnotationDbi::select type in GO select
GO.db AnnotationDbi
updated 3.8 years ago by • 0 • written 3.9 years ago by ▴ 40
0
votes
3
replies
1.6k
views
Error using old ensembldb annotations with R 4.0 +
anno EnsDb.Hsapiens.v79 ensDb.HSapiens.v92 AnnotationDbi ensembldb
3.9 years ago rbenel ▴ 50
1
vote
2
replies
2.2k
views
Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db.
org.Mm.eg.db AnnotationDbi
updated 3.9 years ago by 68k • written 3.9 years ago by ▴ 30
1
vote
2
replies
1.6k
views
What are these genes ? [How to get Ensembl IDs for them]
AnnotationDbi biomaRt
updated 3.9 years ago by ▴ 30 • written 3.9 years ago by • 0
3
votes
1
reply
1.9k
views
[PrimeView] Affymetrix Human Gene Expression Array
AnnotationDbi [PrimeView]AffymetrixHumanGeneExpressionArray
updated 4.0 years ago by ★ 4.1k • written 4.0 years ago by • 0
1
vote
2
replies
3.9k
views
mapping mouse ENSEMBL ids to human gene symbol
Annotation AnnotationDbi annotate
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
0
votes
1
reply
1.6k
views
failing to install the package org.Hs.eg.db in R (version 4.0.5 )
AnnotationDbi org.Hs.eg
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
1
vote
2
replies
2.2k
views
trouble with ENSEMBL ids for Org.Ss.eg.db
Annotation org.Ss.eg.db AnnotationDbi
4.1 years ago carine.genet • 0
6
votes
6
replies
3.3k
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
4.1 years ago svlachavas ▴ 840
5
votes
3
replies
3.6k
views
Get the latest gene name from Entrez ID
AnnotationDbi org.Hs.eg.db
4.3 years ago sgupt46 ▴ 10
0
votes
5
replies
1.4k
views
annotaton hub will not load in R4.04 RStudio3.12
AnnotationDbi
written 4.3 years ago by • 0
1
vote
5
replies
1.6k
views
install Annotation Packages BSgenome.Osativa.MSU.MSU7 failed
Oryza_sativa AnnotationDbi
updated 4.3 years ago by 16k • written 4.3 years ago by • 0
3
votes
2
replies
4.0k
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi ensembldb
4.4 years ago Ezgi ▴ 60
2
votes
3
replies
2.5k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 4.4 years ago by 68k • written 4.4 years ago by ▴ 30
13
votes
12
replies
9.3k
views
From a ENST to ENSG
AnnotationDbi
4.4 years ago suxxa ▴ 20
3
votes
2
replies
2.8k
views
how to use select() to retrieve GO Biological Process Ancestors?
GO.db AnnotationDbi
updated 4.4 years ago by 25k • written 4.4 years ago by ★ 4.1k
4
votes
2
replies
2.1k
views
ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
AnnotationDbi EnsDb.Hsapiens org.Hs.eg.db
updated 4.5 years ago by ★ 2.1k • written 4.5 years ago by • 0
5
votes
7
replies
3.7k
views
Duplicated ENTREZID gene annotations org.Hs.eg.db
ENTREZID SYMBOL AnnotationDbi org.Hs.eg.db
updated 4.5 years ago by 52k • written 4.5 years ago by • 0
6
votes
4
replies
3.4k
views
Annotation with org.Hs.eg.db Genome Build 38
AnnotationDbi org.Hs.eg.db
4.6 years ago Bine ▴ 50
2
votes
3
replies
2.8k
views
Convert Refseq Protein IDs to UniProt IDs
AnnotationDbi
4.6 years ago sgupt46 ▴ 10
5
votes
3
replies
3.7k
views
Gene conversion from SYMBOL to ENTREZ using AnnotationDbi doesn't convert some of the genes
AnnotationDbi org.Hs.eg.db
4.6 years ago Emilia ▴ 40
0
votes
7
replies
11k
views
AnnotationDbi Errors: unable to find an inherited method for function 'select' for signature 'character'.
AnnotationDbi
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
0
votes
4
replies
2.2k
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 5.1 years ago by 68k • written 5.1 years ago by • 0
4
votes
5
replies
2.5k
views
makeOrgPackage - ERROR: Two fields in the source DB have the same name
software error AnnotationForge AnnotationDbi
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
1
vote
5
replies
4.1k
views
Is org.Mm.eg.db updated to mus musculus version 99?
org.Mm.eg.db AnnotationDbi
5.2 years ago kavator ▴ 30
50 results • Page 1 of 1
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Comment: Heatmap of the Count Matrix by gta5movilecom • 0
Using it for the top 20 genes in the heatmap highlights high-expression genes, but may miss out on variance-driven patterns. If you want to…
Answer: Regarding the issue of background genes in enrichment analysis by ATpoint ★ 4.9k
It should imo be the genes that were eligable to yield a "significant" result in your analysis. So, if you test set is derived from differe…
Comment: Applying lmFit(), eBayes() and topTable() for modeling associations between NMR- by Gordon Smyth 52k
> How do these logFC values compare to standard effect sizes derived using a basic regression model like lm()? Exactly the same. Both soft…
Comment: Applying lmFit(), eBayes() and topTable() for modeling associations between NMR- by anni • 0
Ok, thanks! I have just a couple more questions: 1. Based on the [limma User's Guide][1], for binary predictors like overweight, I have i…
Comment: Online workshop "Working with ChatGPT in R" 2023-03-09 by tnaru607 • 0
Thanks for sharing your workflow and benchmarking approach - very informative! I've been experimenting with AI-assisted tools recently, es…
Votes
Answer: I would like to perform differential expression analysis of lncRNAs using DESeq2
I would like to perform differential expression analysis of lncRNAs using DESeq2 and edgeR.
Answer: ExperimentHub full metadata
Answer: AnnotationHub/ExperimentHub resources backup
Answer: ExperimentHub full metadata
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