Showing : AnnotationDbi • reset
0
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420
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org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key
MAMDC4 org.Ss.eg.db AnnotationDbi
written 5 months ago by • 0
0
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3
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293
views
A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::select()
org.Ss.eg.db AnnotationDbi
written 4 months ago by • 0
3
votes
9
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2.4k
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 11 months ago by • 0 • written 12 months ago by • 0
2
votes
3
replies
1.9k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 13 months ago by 68k • written 13 months ago by ▴ 10
0
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2
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1.0k
views
GOstats kegg analysis in wheat - help - none of the objects in the first column are legitimate kegg ids (but they are)
AnnotationDbi GOstats
14 months ago GV Yoshikawa • 0
5
votes
13
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2.5k
views
Installing annotation package in locally
AnnotationDbi AnnotationHub Annotation AnnotationForge
15 months ago KABILAN • 0
0
votes
1
reply
594
views
how do I convert an Ilumn IDREF to a CPG loci
AnnotationDbi Annotation annotation BiologicalQuestion
updated 15 months ago by 68k • written 15 months ago by • 0
2
votes
2
replies
629
views
SAS token for Annotation package
AnnotationDbi AnnotationForge
15 months ago KABILAN • 0
0
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3
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1.7k
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
17 months ago Anna • 0
5
votes
7
replies
3.7k
views
Mapping Between GenBank ID's and Uniprot
UniProt.ws AnnotationDbi
written 18 months ago by • 0
0
votes
0
replies
819
views
Improving Gene Matching for CIBERSORT Deconvolution with Monaco Reference Matrix in Bulk RNA-Seq
DeconRNASeq AnnotationDbi org.Hs.eg.db
18 months ago chunglee13 • 0
2
votes
17
replies
4.7k
views
Problem installing package, version of dependency issue
AnnotationDbi GO.db
updated 2.0 years ago by ▴ 760 • written 2.0 years ago by ▴ 50
2
votes
4
replies
2.5k
views
Annotation Dbi Error: unable to find an inherited method for function 'x' for signature "MaskedBSgenome"
BSgenome.Hsapiens.UCSC.hg19 AnnotationDbi
2.3 years ago Erica • 0
0
votes
1
reply
1.2k
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 2.8 years ago by 68k • written 2.8 years ago by • 0
0
votes
0
replies
1.2k
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb AnnotationDbi Annotation
2.8 years ago ahiser • 0
0
votes
1
reply
1.6k
views
Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 3.0 years ago by 68k • written 3.0 years ago by ▴ 50
2
votes
3
replies
2.7k
views
org.Hs.eg.db gives more than one ENTREZID for a gene symbol
org.Hs.eg.db AnnotationDbi
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
votes
3
replies
1.5k
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
votes
1
reply
1.1k
views
Share Annotation Packages
OrgDb AnnotationDbi
updated 3.3 years ago by 4.3k • written 3.3 years ago by • 0
2
votes
3
replies
4.0k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 3.3 years ago by ▴ 150 • written 3.3 years ago by ▴ 10
0
votes
1
reply
1.9k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
0
votes
1
reply
1.6k
views
Bioconducter can not be installed on latest RStudio
AnnotationDbi biomaRt Bioconductor
updated 3.6 years ago by ★ 6.6k • written 3.6 years ago by • 0
2
votes
3
replies
3.1k
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 2.4 years ago by 68k • written 3.7 years ago by ▴ 70
2
votes
5
replies
4.1k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
3.7 years ago nhaus ▴ 70
0
votes
1
reply
2.4k
views
Converting gene symbols to entrez ID
AnnotationDbi org.Mm.eg.db
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
0
votes
2
replies
2.5k
views
AnnotationDbi
AnnotationDbi
4.2 years ago Bogdan ▴ 670
3
votes
1
reply
3.4k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
1
vote
6
replies
3.4k
views
what's the difference between this two AnnotationDbi::select type in GO select
GO.db AnnotationDbi
updated 4.4 years ago by • 0 • written 4.4 years ago by ▴ 40
0
votes
3
replies
1.8k
views
Error using old ensembldb annotations with R 4.0 +
anno EnsDb.Hsapiens.v79 ensDb.HSapiens.v92 AnnotationDbi ensembldb
4.5 years ago • updated 4.4 years ago rbenel ▴ 50
1
vote
2
replies
2.5k
views
Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db.
org.Mm.eg.db AnnotationDbi
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 30
1
vote
2
replies
1.8k
views
What are these genes ? [How to get Ensembl IDs for them]
AnnotationDbi biomaRt
updated 4.5 years ago by ▴ 30 • written 4.5 years ago by • 0
3
votes
1
reply
2.1k
views
[PrimeView] Affymetrix Human Gene Expression Array
AnnotationDbi [PrimeView]AffymetrixHumanGeneExpressionArray
updated 4.5 years ago by ★ 4.1k • written 4.5 years ago by • 0
1
vote
2
replies
4.5k
views
mapping mouse ENSEMBL ids to human gene symbol
Annotation AnnotationDbi annotate
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
0
votes
1
reply
1.8k
views
failing to install the package org.Hs.eg.db in R (version 4.0.5 )
AnnotationDbi org.Hs.eg
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
1
vote
2
replies
2.5k
views
trouble with ENSEMBL ids for Org.Ss.eg.db
Annotation org.Ss.eg.db AnnotationDbi
4.6 years ago carine.genet • 0
6
votes
6
replies
3.8k
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
4.7 years ago svlachavas ▴ 840
5
votes
3
replies
4.1k
views
Get the latest gene name from Entrez ID
AnnotationDbi org.Hs.eg.db
4.8 years ago sgupt46 ▴ 10
0
votes
5
replies
1.6k
views
annotaton hub will not load in R4.04 RStudio3.12
AnnotationDbi
written 4.9 years ago by • 0
1
vote
5
replies
1.8k
views
install Annotation Packages BSgenome.Osativa.MSU.MSU7 failed
Oryza_sativa AnnotationDbi
updated 4.9 years ago by 16k • written 4.9 years ago by • 0
3
votes
2
replies
4.6k
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi ensembldb
5.0 years ago Ezgi ▴ 60
2
votes
3
replies
2.9k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 30
13
votes
12
replies
10k
views
From a ENST to ENSG
AnnotationDbi
5.0 years ago suxxa ▴ 20
3
votes
2
replies
3.2k
views
how to use select() to retrieve GO Biological Process Ancestors?
GO.db AnnotationDbi
updated 5.0 years ago by 25k • written 5.0 years ago by ★ 4.1k
4
votes
2
replies
2.4k
views
ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
AnnotationDbi EnsDb.Hsapiens org.Hs.eg.db
updated 5.0 years ago by ★ 2.1k • written 5.0 years ago by • 0
5
votes
7
replies
4.0k
views
Duplicated ENTREZID gene annotations org.Hs.eg.db
ENTREZID SYMBOL AnnotationDbi org.Hs.eg.db
updated 5.0 years ago by 53k • written 5.0 years ago by • 0
6
votes
4
replies
4.1k
views
Annotation with org.Hs.eg.db Genome Build 38
AnnotationDbi org.Hs.eg.db
5.1 years ago Bine ▴ 50
2
votes
3
replies
3.0k
views
Convert Refseq Protein IDs to UniProt IDs
AnnotationDbi
5.1 years ago sgupt46 ▴ 10
5
votes
3
replies
4.3k
views
Gene conversion from SYMBOL to ENTREZ using AnnotationDbi doesn't convert some of the genes
AnnotationDbi org.Hs.eg.db
5.1 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 5.5 years ago by 68k • written 5.5 years ago by • 0
0
votes
4
replies
2.4k
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 5.6 years ago by 68k • written 5.6 years ago by • 0
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Votes
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A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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