Showing : AnnotationDbi • reset
19
votes
6
replies
23k
views
How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
rnaseq annotationdbi
updated 5.6 years ago by ★ 6.7k • written 5.7 years ago by ▴ 70
11
votes
12
replies
1.6k
views
From a ENST to ENSG
AnnotationDbi
16 months ago • updated 15 months ago suxxa ▴ 20
8
votes
12
replies
2.5k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 4.7 years ago by ★ 1.9k • written 4.7 years ago by • 0
8
votes
2
replies
1.5k
views
How to deal with Affymetrix GeneChip probeids that map to multiple genes
hta20sttranscriptcluster.db probe mapping annotation pd.hta.2.0 annotationdbi
updated 5.7 years ago by 60k • written 5.7 years ago by ▴ 20
7
votes
11
replies
5.6k
views
Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.probes
edgeR limma annotationhub kegga annotationdbi
updated 5.9 years ago by ▴ 20 • written 6.2 years ago by ▴ 20
6
votes
6
replies
739
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
12 months ago svlachavas ▴ 780
5
votes
7
replies
841
views
Concatenation of Bimap
AnnotationDbi Concatenate
updated 6.5 years ago by 60k • written 6.5 years ago by ★ 1.5k
5
votes
22
replies
4.3k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 5.9 years ago by ▴ 990 • written 7.3 years ago by • 0
5
votes
7
replies
776
views
Duplicated ENTREZID gene annotations org.Hs.eg.db
ENTREZID SYMBOL AnnotationDbi org.Hs.eg.db
updated 16 months ago by 45k • written 16 months ago by • 0
5
votes
6
replies
1.3k
views
Is mapId supposed to concatenate multiVals?
annotationdbi ensembldb
updated 5.0 years ago by ★ 1.9k • written 5.0 years ago by 13k
5
votes
3
replies
2.6k
views
Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapiens/Mus.musculus?
homo.sapiens annotationdbi
updated 4.5 years ago by ★ 1.9k • written 4.5 years ago by ▴ 40
5
votes
11
replies
878
views
an error in BioMart regarding gene annotations
biomart AnnotationDbi
updated 3.9 years ago by ▴ 50 • written 3.9 years ago by ▴ 640
5
votes
11
replies
654
views
Inconsistent data within org.Sc.sgd.db package
org.Sc.sgd.db AnnotationDbi
updated 3 months ago by • 0 • written 2.3 years ago by • 0
4
votes
1
reply
1.1k
views
Retrieving all genes related a go term
go R annotationdbi biomart
updated 4.7 years ago by 60k • written 4.7 years ago by ▴ 40
4
votes
1
reply
4.7k
views
Finding orthologous human/mouse ENSEMBL IDs
human mouse ensembl annotationdbi homologue
5.0 years ago • updated 4.9 years ago Keith Hughitt ▴ 150
4
votes
5
replies
771
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 3.1 years ago by 60k • written 3.2 years ago by ▴ 10
4
votes
8
replies
3.1k
views
Annotating DEseq output using AnnotationDbi mapIds and most results say NA
AnnotationDbi mapIds org.Mm.eg.db ENSEMBLTRANS
updated 5.4 years ago by 60k • written 5.4 years ago by ▴ 10
4
votes
2
replies
1.3k
views
mapIds to get GO terms
annotationdbi go.db
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 10
4
votes
3
replies
543
views
Gene conversion from SYMBOL to ENTREZ using AnnotationDbi doesn't convert some of the genes
AnnotationDbi org.Hs.eg.db
18 months ago Emilia ▴ 30
4
votes
2
replies
529
views
ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
AnnotationDbi EnsDb.Hsapiens org.Hs.eg.db
updated 16 months ago by ★ 1.9k • written 16 months ago by • 0
4
votes
5
replies
777
views
makeOrgPackage - ERROR: Two fields in the source DB have the same name
software error AnnotationForge AnnotationDbi
updated 2.0 years ago by 60k • written 2.0 years ago by • 0
3
votes
4
replies
626
views
Annotation with org.Hs.eg.db Genome Build 38
AnnotationDbi org.Hs.eg.db
17 months ago Bine ▴ 20
3
votes
6
replies
1.2k
views
Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
annotation ensembl annotationdbi
3.9 years ago vd4mmind • 0
3
votes
4
replies
1.2k
views
DGE matrix annotation
DGE DESeq2 AnnotationDbi
updated 3.6 years ago by 60k • written 3.6 years ago by • 0
3
votes
1
reply
317
views
[PrimeView] Affymetrix Human Gene Expression Array
AnnotationDbi [PrimeView]AffymetrixHumanGeneExpressionArray
updated 10 months ago by ★ 3.2k • written 10 months ago by • 0
3
votes
3
replies
514
views
Get the latest gene name from Entrez ID
AnnotationDbi org.Hs.eg.db
14 months ago sgupt46 • 0
3
votes
5
replies
1.0k
views
Selecting few ids from reactome.db
annotationdbi reactome.db bug
updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 660
3
votes
5
replies
967
views
GO.db installation fails (MacOS, AnnotationDbi, R3.5.0)
GO bioclite R3.5 mac os x annotationdbi
updated 4.0 years ago by 25k • written 4.0 years ago by ▴ 30
3
votes
2
replies
659
views
select With Regular Expression
annotationdbi Wildcard
updated 5.9 years ago by ★ 1.9k • written 5.9 years ago by ★ 1.5k
3
votes
2
replies
445
views
how to use select() to retrieve GO Biological Process Ancestors?
GO.db AnnotationDbi
updated 16 months ago by 25k • written 16 months ago by ★ 3.2k
3
votes
5
replies
2.0k
views
Map TxDb.Hsapiens.UCSC.hg19.knownGene TXID keys to ENSEMBL transcript ID or Refseq ID
annotationdbi
updated 5.4 years ago by 60k • written 5.4 years ago by ▴ 10
3
votes
18
replies
1.9k
views
Annotating codelink data file
r codelink annotation annotationdbi
updated 7.1 years ago by ▴ 760 • written 7.1 years ago by ▴ 260
3
votes
2
replies
681
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi ensembldb
15 months ago Ezgi ▴ 30
3
votes
2
replies
1.1k
views
Trouble getting probe ID info from mouse4302.db annotation package with a specific RefSeq ID.
annotationdbi mouse4302 affymetrixchip annotationdata R
updated 6.5 years ago by 60k • written 6.5 years ago by • 0
2
votes
2
replies
2.4k
views
failing to install the package org.Hs.eg.db in R (version 3.5.2 )
org.Hs.eg.db AnnotationDbi
updated 3.2 years ago by 25k • written 3.2 years ago by • 0
2
votes
1
reply
72
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 8 days ago by 60k • written 8 days ago by • 0
2
votes
1
reply
560
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 8 months ago by 60k • written 8 months ago by • 0
2
votes
2
replies
2.4k
views
problem using AnnotationDbi
annotationdbi bioconductor
4.3 years ago h72ghorashi • 0
2
votes
5
replies
160
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
17 days ago • updated 16 days ago nhaus • 0
2
votes
5
replies
1.1k
views
building a new annotation
Annotation AnnBuilder AnnotationDbi Annotation AnnBuilder AnnotationDbi
updated 13.2 years ago by ★ 7.2k • written 13.2 years ago by ▴ 10
2
votes
1
reply
1.1k
views
Missing SYMBOL keytype in EnsDb.Hsapiens.v75
annotationdbi EnsDb.Hsapiens.v75
updated 5.8 years ago by ★ 1.9k • written 5.8 years ago by ▴ 10
2
votes
3
replies
567
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 16 months ago by 60k • written 16 months ago by ▴ 10
2
votes
3
replies
548
views
Convert Refseq Protein IDs to UniProt IDs
AnnotationDbi
17 months ago sgupt46 • 0
2
votes
1
reply
3.1k
views
Find correct annotation for specific agilent platforms Whole Human Genome Microarray 4x44K
agilent whole Human Genome Microarray 4X44K annotationdbi bioconductor
6.6 years ago Konstantinos Yeles ▴ 70
2
votes
3
replies
1.9k
views
org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
chippeakanno annotationdbi
updated 4.6 years ago by • 0 • written 6.6 years ago by • 0
2
votes
2
replies
1.3k
views
Cannot retrieve Annotations for a GENEID from Homo.sapiens
annotation annotationdbi homo.sapiens
updated 7.5 years ago by 60k • written 7.5 years ago by ▴ 50
2
votes
4
replies
1.9k
views
Problems during the installation of AnnotationDbi and pasilla
AnnotationDbi
updated 7.6 years ago by ▴ 200 • written 7.6 years ago by • 0
2
votes
3
replies
665
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport tximeta AnnotationDbi
2.9 years ago Benjamin • 0
1
vote
9
replies
725
views
AnnotationDbi: Select - Join order
AnnotationDbi
3.3 years ago faustfrankenstein • 0
1
vote
2
replies
597
views
SYMBOL is not the official MGI gene symbol?
org.mm.eg.db annotationdbi
updated 3.8 years ago by 60k • written 3.8 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: edgeR : results from goana and kegga functions show opposite sig. p-value by sharvari gujja ▴ 30
Thank you so much!
Comment: Subsetting operation on CompressedGRangesList object 'x' produces a result tha by Hervé Pagès 15k
Hi Jiping, Sorry for the slow response and thanks for providing those details. They allowed me to reproduce the problem and to come up wit…
Answer: Trouble with detecting AS events using ASpediaFI by rbqlsrbqls56 • 0
Assuming you downloaded "Homo_sapiens.GRCh38.104.gtf" from the Ensembl website, the gene model contains reference chromosomes (chr1-22, X, …
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value by James W. MacDonald 60k
It is not a valid assumption that a GO term and a KEGG term that appear to be the same are actually the same. ``` > library(org.Hs.eg.d…
Comment: help please！ by shepherl 3.1k
what is the result of `.libPaths()` and `"AnnotationDbi" %in% rownames(installed.packages())`
Votes
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
Answer: paired analysis : return data matrix with indvidual/subject effects eliminated.
DESeq2: likelihood ratio test interpretation, multifactor
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
Answer: GDCprepare of RNAseq counts produces error
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