Showing : annotationdbi • reset
3
votes
9
replies
807
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 26 days ago by • 0 • written 7 weeks ago by • 0
2
votes
3
replies
1.3k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 12 weeks ago by 68k • written 12 weeks ago by ▴ 10
0
votes
2
replies
792
views
GOstats kegg analysis in wheat - help - none of the objects in the first column are legitimate kegg ids (but they are)
AnnotationDbi GOstats
3 months ago GV Yoshikawa • 0
5
votes
13
replies
1.8k
views
Installing annotation package in locally
AnnotationDbi AnnotationHub Annotation AnnotationForge
4 months ago KABILAN • 0
0
votes
1
reply
308
views
how do I convert an Ilumn IDREF to a CPG loci
AnnotationDbi Annotation annotation BiologicalQuestion
updated 4 months ago by 68k • written 5 months ago by • 0
2
votes
2
replies
305
views
SAS token for Annotation package
AnnotationDbi AnnotationForge
5 months ago KABILAN • 0
0
votes
3
replies
899
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
6 months ago Anna • 0
5
votes
7
replies
1.5k
views
Mapping Between GenBank ID's and Uniprot
UniProt.ws AnnotationDbi
written 8 months ago by • 0
0
votes
0
replies
436
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
2.9k
views
Problem installing package, version of dependency issue
AnnotationDbi GO.db
updated 13 months ago by ▴ 760 • written 13 months ago by ▴ 50
2
votes
4
replies
1.8k
views
Annotation Dbi Error: unable to find an inherited method for function 'x' for signature "MaskedBSgenome"
BSgenome.Hsapiens.UCSC.hg19 AnnotationDbi
16 months ago Erica • 0
0
votes
1
reply
845
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
863
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb AnnotationDbi Annotation
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
2.1k
views
org.Hs.eg.db gives more than one ENTREZID for a gene symbol
org.Hs.eg.db AnnotationDbi
updated 2.1 years ago by 68k • written 2.1 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 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
1
reply
928
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
3.3k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 2.4 years ago by ▴ 150 • written 2.4 years ago by ▴ 10
0
votes
1
reply
1.6k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
votes
1
reply
1.2k
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
2.3k
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 18 months ago by 68k • written 2.8 years ago by ▴ 70
2
votes
5
replies
3.0k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
2.8 years ago nhaus ▴ 70
0
votes
1
reply
1.9k
views
Converting gene symbols to entrez ID
AnnotationDbi org.Mm.eg.db
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
votes
2
replies
2.1k
views
AnnotationDbi
AnnotationDbi
3.3 years ago Bogdan ▴ 670
3
votes
1
reply
2.8k
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
2.6k
views
what's the difference between this two AnnotationDbi::select type in GO select
GO.db AnnotationDbi
updated 3.5 years ago by • 0 • written 3.5 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 3.6 years ago by • 0
3
votes
1
reply
1.7k
views
[PrimeView] Affymetrix Human Gene Expression Array
AnnotationDbi [PrimeView]AffymetrixHumanGeneExpressionArray
updated 3.6 years ago by ★ 4.1k • written 3.6 years ago by • 0
1
vote
2
replies
3.4k
views
mapping mouse ENSEMBL ids to human gene symbol
Annotation AnnotationDbi annotate
updated 3.6 years ago by 68k • written 3.6 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 3.7 years ago by 68k • written 3.7 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
3.7 years ago carine.genet • 0
6
votes
6
replies
3.0k
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
3.3k
views
Get the latest gene name from Entrez ID
AnnotationDbi org.Hs.eg.db
3.9 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
3.5k
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 4.1 years ago by ▴ 30
13
votes
12
replies
8.6k
views
From a ENST to ENSG
AnnotationDbi
4.1 years ago suxxa ▴ 20
3
votes
2
replies
2.6k
views
how to use select() to retrieve GO Biological Process Ancestors?
GO.db AnnotationDbi
updated 4.1 years ago by 25k • written 4.1 years ago by ★ 4.1k
4
votes
2
replies
1.9k
views
ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
AnnotationDbi EnsDb.Hsapiens org.Hs.eg.db
updated 4.1 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 4.1 years ago by 52k • written 4.2 years ago by • 0
6
votes
4
replies
2.9k
views
Annotation with org.Hs.eg.db Genome Build 38
AnnotationDbi org.Hs.eg.db
4.2 years ago Bine ▴ 50
2
votes
3
replies
2.6k
views
Convert Refseq Protein IDs to UniProt IDs
AnnotationDbi
4.2 years ago sgupt46 ▴ 10
5
votes
3
replies
3.3k
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
2.0k
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 4.7 years ago by 68k • written 4.7 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 4.8 years ago by 68k • written 4.8 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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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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