Showing : AnnotationDbi • reset
3
votes
9
replies
904
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 6 weeks ago by • 0 • written 10 weeks ago by • 0
2
votes
3
replies
1.4k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 3 months ago by 68k • written 3 months ago by ▴ 10
0
votes
2
replies
811
views
GOstats kegg analysis in wheat - help - none of the objects in the first column are legitimate kegg ids (but they are)
AnnotationDbi GOstats
4 months ago GV Yoshikawa • 0
5
votes
13
replies
1.9k
views
Installing annotation package in locally
AnnotationDbi AnnotationHub Annotation AnnotationForge
5 months ago KABILAN • 0
0
votes
1
reply
328
views
how do I convert an Ilumn IDREF to a CPG loci
AnnotationDbi Annotation annotation BiologicalQuestion
updated 5 months ago by 68k • written 5 months ago by • 0
2
votes
2
replies
332
views
SAS token for Annotation package
AnnotationDbi AnnotationForge
5 months ago KABILAN • 0
0
votes
3
replies
991
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
7 months ago Anna • 0
5
votes
7
replies
1.6k
views
Mapping Between GenBank ID's and Uniprot
UniProt.ws AnnotationDbi
written 8 months ago by • 0
0
votes
0
replies
459
views
Improving Gene Matching for CIBERSORT Deconvolution with Monaco Reference Matrix in Bulk RNA-Seq
DeconRNASeq AnnotationDbi org.Hs.eg.db
8 months ago chunglee13 • 0
2
votes
17
replies
3.1k
views
Problem installing package, version of dependency issue
AnnotationDbi GO.db
updated 14 months ago by ▴ 760 • written 14 months ago by ▴ 50
2
votes
4
replies
1.9k
views
Annotation Dbi Error: unable to find an inherited method for function 'x' for signature "MaskedBSgenome"
BSgenome.Hsapiens.UCSC.hg19 AnnotationDbi
17 months ago Erica • 0
0
votes
1
reply
872
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 23 months ago by 68k • written 23 months ago by • 0
0
votes
0
replies
875
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb AnnotationDbi Annotation
24 months ago • updated 23 months ago ahiser • 0
0
votes
1
reply
1.3k
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 50
2
votes
3
replies
2.2k
views
org.Hs.eg.db gives more than one ENTREZID for a gene symbol
org.Hs.eg.db AnnotationDbi
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
3
replies
1.1k
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
1
reply
937
views
Share Annotation Packages
OrgDb AnnotationDbi
updated 2.4 years ago by 4.1k • written 2.4 years ago by • 0
2
votes
3
replies
3.4k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 2.5 years ago by ▴ 150 • written 2.5 years ago by ▴ 10
0
votes
1
reply
1.6k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
0
votes
1
reply
1.3k
views
Bioconducter can not be installed on latest RStudio
AnnotationDbi biomaRt Bioconductor
updated 2.7 years ago by ★ 6.6k • written 2.7 years ago by • 0
2
votes
3
replies
2.4k
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 19 months ago by 68k • written 2.9 years ago by ▴ 70
2
votes
5
replies
3.1k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
2.9 years ago nhaus ▴ 70
0
votes
1
reply
2.0k
views
Converting gene symbols to entrez ID
AnnotationDbi org.Mm.eg.db
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
votes
2
replies
2.1k
views
AnnotationDbi
AnnotationDbi
3.4 years ago Bogdan ▴ 670
3
votes
1
reply
2.9k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
1
vote
6
replies
2.7k
views
what's the difference between this two AnnotationDbi::select type in GO select
GO.db AnnotationDbi
updated 3.6 years ago by • 0 • written 3.6 years ago by ▴ 40
0
votes
3
replies
1.4k
views
Error using old ensembldb annotations with R 4.0 +
anno EnsDb.Hsapiens.v79 ensDb.HSapiens.v92 AnnotationDbi ensembldb
3.6 years ago rbenel ▴ 40
1
vote
2
replies
2.0k
views
Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db.
org.Mm.eg.db AnnotationDbi
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 30
1
vote
2
replies
1.5k
views
What are these genes ? [How to get Ensembl IDs for them]
AnnotationDbi biomaRt
updated 3.6 years ago by ▴ 30 • written 3.7 years ago by • 0
3
votes
1
reply
1.7k
views
[PrimeView] Affymetrix Human Gene Expression Array
AnnotationDbi [PrimeView]AffymetrixHumanGeneExpressionArray
updated 3.7 years ago by ★ 4.1k • written 3.7 years ago by • 0
1
vote
2
replies
3.5k
views
mapping mouse ENSEMBL ids to human gene symbol
Annotation AnnotationDbi annotate
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
votes
1
reply
1.5k
views
failing to install the package org.Hs.eg.db in R (version 4.0.5 )
AnnotationDbi org.Hs.eg
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
1
vote
2
replies
2.0k
views
trouble with ENSEMBL ids for Org.Ss.eg.db
Annotation org.Ss.eg.db AnnotationDbi
3.8 years ago carine.genet • 0
6
votes
6
replies
3.1k
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
3.8 years ago svlachavas ▴ 840
5
votes
3
replies
3.4k
views
Get the latest gene name from Entrez ID
AnnotationDbi org.Hs.eg.db
4.0 years ago sgupt46 ▴ 10
0
votes
5
replies
1.3k
views
annotaton hub will not load in R4.04 RStudio3.12
AnnotationDbi
written 4.0 years ago by • 0
1
vote
5
replies
1.5k
views
install Annotation Packages BSgenome.Osativa.MSU.MSU7 failed
Oryza_sativa AnnotationDbi
updated 4.0 years ago by 16k • written 4.0 years ago by • 0
3
votes
2
replies
3.6k
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi ensembldb
4.1 years ago Ezgi ▴ 60
2
votes
3
replies
2.3k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 4.1 years ago by 68k • written 4.2 years ago by ▴ 30
13
votes
12
replies
8.8k
views
From a ENST to ENSG
AnnotationDbi
4.2 years ago • updated 4.1 years ago suxxa ▴ 20
3
votes
2
replies
2.7k
views
how to use select() to retrieve GO Biological Process Ancestors?
GO.db AnnotationDbi
updated 4.2 years ago by 25k • written 4.2 years ago by ★ 4.1k
4
votes
2
replies
2.0k
views
ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
AnnotationDbi EnsDb.Hsapiens org.Hs.eg.db
updated 4.2 years ago by ★ 2.1k • written 4.2 years ago by • 0
5
votes
7
replies
3.4k
views
Duplicated ENTREZID gene annotations org.Hs.eg.db
ENTREZID SYMBOL AnnotationDbi org.Hs.eg.db
updated 4.2 years ago by 52k • written 4.2 years ago by • 0
6
votes
4
replies
3.0k
views
Annotation with org.Hs.eg.db Genome Build 38
AnnotationDbi org.Hs.eg.db
4.3 years ago Bine ▴ 50
2
votes
3
replies
2.6k
views
Convert Refseq Protein IDs to UniProt IDs
AnnotationDbi
4.3 years ago sgupt46 ▴ 10
5
votes
3
replies
3.4k
views
Gene conversion from SYMBOL to ENTREZ using AnnotationDbi doesn't convert some of the genes
AnnotationDbi org.Hs.eg.db
4.3 years ago Emilia ▴ 40
0
votes
7
replies
10k
views
AnnotationDbi Errors: unable to find an inherited method for function 'select' for signature 'character'.
AnnotationDbi
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
0
votes
4
replies
2.1k
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 4.8 years ago by 68k • written 4.8 years ago by • 0
4
votes
5
replies
2.4k
views
makeOrgPackage - ERROR: Two fields in the source DB have the same name
software error AnnotationForge AnnotationDbi
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
1
vote
5
replies
3.5k
views
Is org.Mm.eg.db updated to mus musculus version 99?
org.Mm.eg.db AnnotationDbi
4.9 years ago kavator ▴ 30
50 results • Page 1 of 1
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Answer: best way to grouping GSM belonging to different datasets (with different platfor by James W. MacDonald 68k
The only defensible way is to make comparisons within experiments and then do a meta-analysis. But that assumes you have identified multipl…
Comment: DESeq2 estimateSizeFactors with control genes by sofia.rigou • 0
I am also trying to use this function to estimate sizefactor based on RT-dPCR data but estimateSizeFactor only takes integers. Should I mul…
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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