Showing : annotationdbi • reset
2
votes
17
replies
966
views
Problem installing package, version of dependency issue
AnnotationDbi GO.db
updated 12 weeks ago by ▴ 730 • written 3 months ago by ▴ 50
2
votes
4
replies
907
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
0
votes
1
reply
520
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
494
views
AnnotationDbi Error: PROSITE is defunct.
ChipDb AnnotationDbi Annotation
12 months ago ahiser • 0
0
votes
1
reply
786
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
731
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
666
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 18 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 19 months ago by 65k • written 19 months ago by • 0
0
votes
1
reply
871
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
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
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
1.4k
views
Converting gene symbols to entrez ID
AnnotationDbi org.Mm.eg.db
updated 2.0 years ago by 65k • written 2.0 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
992
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 2.7 years ago by ★ 3.9k • written 2.7 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
1.1k
views
failing to install the package org.Hs.eg.db in R (version 4.0.5 )
AnnotationDbi org.Hs.eg
updated 2.8 years ago by 65k • written 2.8 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
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
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
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
2
votes
3
replies
1.6k
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
13
votes
12
replies
6.5k
views
From a ENST to ENSG
AnnotationDbi
3.2 years ago suxxa ▴ 20
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 3.2 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 • updated 3.3 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 3.9 years ago by 65k • written 3.9 years ago by • 0
1
vote
5
replies
2.4k
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
875
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 4.0 years ago by 25k • written 4.0 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 • updated 4.0 years ago CUCIO199 • 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
789
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
1.0k
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
4
votes
5
replies
1.5k
views
Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens.UCSC.hg19.knownGene
ensembl cdschrom org.Hs.eg.db AnnotationDbi SingleCellExperiment
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 10
0
votes
5
replies
1.5k
views
hyperGTest not working on custom annotation package
GOstats AnnotationDbi GO.db
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
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Comment: Input Question for deseq.r by ATpoint ★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present by ATpoint ★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded by ATpoint ★ 4.0k
```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…
Comment: DESeq2 setting significant p-value by Dev • 0
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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