Showing : annotationdbi • reset
19
votes
6
replies
46k
views
How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
rnaseq annotationdbi
updated 8.6 years ago by ★ 6.8k • written 8.7 years ago by ▴ 70
0
votes
3
replies
12k
views
trouble using select() to get all GO terms when have duplicate query IDs
AnnotationDbi
updated 9.5 years ago by 68k • written 9.5 years ago by ★ 2.0k
1
vote
2
replies
12k
views
select() gene in db not working although key exists
annotationdbi org.mm.eg.db org.dm.eg.db select
10.1 years ago Patrick Schorderet ▴ 20
0
votes
7
replies
11k
views
AnnotationDbi Errors: unable to find an inherited method for function 'select' for signature 'character'.
AnnotationDbi
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
13
votes
12
replies
9.1k
views
From a ENST to ENSG
AnnotationDbi
4.3 years ago suxxa ▴ 20
6
votes
1
reply
8.3k
views
Finding orthologous human/mouse ENSEMBL IDs
human mouse ensembl annotationdbi homologue
7.9 years ago Keith Hughitt ▴ 180
7
votes
11
replies
6.8k
views
Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.probes
edgeR limma annotationhub kegga annotationdbi
updated 8.9 years ago by ▴ 20 • written 9.2 years ago by ▴ 20
3
votes
3
replies
6.3k
views
failing to install the package org.Hs.eg.db in R (version 3.5.2 )
org.Hs.eg.db AnnotationDbi
updated 2.2 years ago by • 0 • written 6.2 years ago by • 0
5
votes
22
replies
6.3k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 8.8 years ago by ★ 1.1k • written 10.3 years ago by • 0
0
votes
14
replies
5.9k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
8.3 years ago • updated 2.7 years ago Jenny Drnevich ★ 2.0k
4
votes
8
replies
5.5k
views
Annotating DEseq output using AnnotationDbi mapIds and most results say NA
AnnotationDbi mapIds org.Mm.eg.db ENSEMBLTRANS
updated 8.4 years ago by 68k • written 8.4 years ago by ▴ 10
0
votes
3
replies
4.9k
views
ERROR: dependency 'AnnotationDbi' is not available for package 'GO.db'
bioconductor R go.db annotationdbi dependency
8.2 years ago Sidi.Ma • 0
0
votes
1
reply
4.8k
views
ERROR: lazy loading failed for package ‘org.Hs.eg.db’
org.hs.eg.db annotationdbi error
updated 10.1 years ago by ★ 8.2k • written 10.1 years ago by • 0
2
votes
1
reply
4.7k
views
Find correct annotation for specific agilent platforms Whole Human Genome Microarray 4x44K
agilent whole Human Genome Microarray 4X44K annotationdbi bioconductor
9.6 years ago Konstantinos Yeles ▴ 80
5
votes
3
replies
4.7k
views
Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapiens/Mus.musculus?
homo.sapiens annotationdbi
updated 7.5 years ago by ★ 2.1k • written 7.5 years ago by ▴ 40
8
votes
12
replies
4.6k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 7.7 years ago by ★ 2.1k • written 7.7 years ago by • 0
1
vote
2
replies
4.3k
views
Error attaching org.Hs.eg.db package
annotationdbi annotation organismdb loadnamespace
10.5 years ago milorobertsmith • 0
3
votes
6
replies
4.0k
views
Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
annotation ensembl annotationdbi
6.9 years ago vd4mmind • 0
2
votes
2
replies
4.0k
views
problem using AnnotationDbi
annotationdbi bioconductor
7.3 years ago h72ghorashi • 0
1
vote
5
replies
3.9k
views
Is org.Mm.eg.db updated to mus musculus version 99?
org.Mm.eg.db AnnotationDbi
5.1 years ago kavator ▴ 30
3
votes
2
replies
3.8k
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi ensembldb
4.3 years ago Ezgi ▴ 60
1
vote
2
replies
3.8k
views
mapping mouse ENSEMBL ids to human gene symbol
Annotation AnnotationDbi annotate
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
5
votes
3
replies
3.6k
views
Gene conversion from SYMBOL to ENTREZ using AnnotationDbi doesn't convert some of the genes
AnnotationDbi org.Hs.eg.db
4.5 years ago Emilia ▴ 40
0
votes
3
replies
3.6k
views
Annotation DB for ArrayStar lncRNA arrays
arraystar lncRNA annotation annotationdbi
updated 9.7 years ago by • 0 • written 10.2 years ago by ▴ 430
5
votes
6
replies
3.6k
views
Is mapId supposed to concatenate multiVals?
annotationdbi ensembldb
updated 8.0 years ago by ★ 2.1k • written 8.0 years ago by ★ 13k
5
votes
7
replies
3.6k
views
Duplicated ENTREZID gene annotations org.Hs.eg.db
ENTREZID SYMBOL AnnotationDbi org.Hs.eg.db
updated 4.4 years ago by 52k • written 4.4 years ago by • 0
5
votes
3
replies
3.6k
views
Get the latest gene name from Entrez ID
AnnotationDbi org.Hs.eg.db
4.2 years ago sgupt46 ▴ 10
2
votes
3
replies
3.6k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 2.6 years ago by ▴ 150 • written 2.7 years ago by ▴ 10
2
votes
17
replies
3.5k
views
Problem installing package, version of dependency issue
AnnotationDbi GO.db
updated 16 months ago by ▴ 760 • written 16 months ago by ▴ 50
3
votes
5
replies
3.5k
views
Map TxDb.Hsapiens.UCSC.hg19.knownGene TXID keys to ENSEMBL transcript ID or Refseq ID
annotationdbi
updated 8.4 years ago by 68k • written 8.4 years ago by ▴ 10
3
votes
18
replies
3.4k
views
Annotating codelink data file
r codelink annotation annotationdbi
updated 10.1 years ago by ▴ 760 • written 10.1 years ago by ▴ 260
2
votes
5
replies
3.4k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
3.0 years ago nhaus ▴ 70
6
votes
4
replies
3.4k
views
Annotation with org.Hs.eg.db Genome Build 38
AnnotationDbi org.Hs.eg.db
4.4 years ago Bine ▴ 50
0
votes
4
replies
3.3k
views
topGO annotations issue
topgo annotationdbi
10.3 years ago willmacnair • 0
9
votes
2
replies
3.3k
views
How to deal with Affymetrix GeneChip probeids that map to multiple genes
hta20sttranscriptcluster.db probe mapping annotation pd.hta.2.0 annotationdbi
updated 8.7 years ago by 68k • written 8.7 years ago by ▴ 20
6
votes
6
replies
3.2k
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
4.0 years ago svlachavas ▴ 840
2
votes
3
replies
3.1k
views
org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
chippeakanno annotationdbi
updated 7.6 years ago by • 0 • written 9.6 years ago by • 0
1
vote
9
replies
3.1k
views
AnnotationDbi: Select - Join order
AnnotationDbi
6.3 years ago faustfrankenstein • 0
3
votes
1
reply
3.0k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
1
vote
4
replies
2.9k
views
biocLite updating problem with Ubuntu 17.10
ubuntu biocgenerics s4vectors IRanges annotationdbi
updated 7.4 years ago by 25k • written 7.4 years ago by • 0
0
votes
1
reply
2.9k
views
GO term as "keytype" in GO.db
GO AnnotationDbi GO AnnotationDbi
updated 12.1 years ago by 6.7k • written 12.1 years ago by ★ 3.4k
1
vote
6
replies
2.8k
views
what's the difference between this two AnnotationDbi::select type in GO select
GO.db AnnotationDbi
updated 3.7 years ago by • 0 • written 3.7 years ago by ▴ 40
3
votes
2
replies
2.8k
views
how to use select() to retrieve GO Biological Process Ancestors?
GO.db AnnotationDbi
updated 4.3 years ago by 25k • written 4.3 years ago by ★ 4.1k
0
votes
2
replies
2.8k
views
Weirdness with the human org.Hs.eg.db annotation database
annotationdbi homo sapiens
updated 10.6 years ago by ★ 7.2k • written 10.6 years ago by ▴ 220
1
vote
3
replies
2.7k
views
Annotate gene counts
annotation RNASeq annotationdbi
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
2
votes
3
replies
2.7k
views
Convert Refseq Protein IDs to UniProt IDs
AnnotationDbi
4.5 years ago • updated 4.4 years ago sgupt46 ▴ 10
2
votes
3
replies
2.6k
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport tximeta AnnotationDbi
5.9 years ago Benjamin • 0
0
votes
6
replies
2.6k
views
Missing as.list generic from AnnotationDbi?
annotate AnnotationDbi annotate AnnotationDbi
updated 10.7 years ago by ★ 2.0k • written 11.9 years ago by ★ 7.9k
0
votes
4
replies
2.6k
views
Installing beadarray
annotate geneplotter beadarray AnnotationDbi annotate geneplotter beadarray AnnotationDbi
updated 17.6 years ago by 21k • written 17.6 years ago by ▴ 270
2
votes
4
replies
2.6k
views
Problems during the installation of AnnotationDbi and pasilla
AnnotationDbi
updated 10.6 years ago by ▴ 200 • written 10.6 years ago by • 0
50 results • Page 1 of 1
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Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k
Probably not. Any given gene may be appended with many different GO terms, so you would end up with something that is not very useful. ``…
Comment: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k
`heatmap.2` is a CRAN package, and that's the relevant issue for this plot. It's got nothing to do with `DESeq2` or any other Bioconductor …
Comment: Limma suqeezeVar by Mengchun • 0
Hi Gordon, Thank you for your reply. I'm working on a proteomics data imputation project, I would like to describe the intensity distribut…
Comment: Heatmap of rnaseq data with z-score scale by giovanna • 0
thank you for your reply. I'm sorry if the question is off topic. the analysis and relative construction of the heatmap was done using bioc…
Answer: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k
Without including the row names for the heatmap, it's impossible to know if the directionality is switched or not. Do note that the orderin…
Votes
Answer: LogFC values in edgeR - w/wo intercept
How to formulate 2 factor nested design in DESeq2
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
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