Showing : OrgDB • reset
1
vote
8
replies
873
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 8 weeks ago by 67k • written 7 months ago by • 0
2
votes
2
replies
779
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 7 months ago by 67k • written 7 months ago by • 0
2
votes
2
replies
763
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 8 months ago by ▴ 10
1
vote
3
replies
732
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo OrgDb convert Organismname RStudio
updated 13 months ago by 67k • written 13 months ago by • 0
2
votes
4
replies
889
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
13 months ago • updated 10 months ago mat149 ▴ 80
0
votes
0
replies
2.4k
views
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
OrgDb
23 months ago hswdl • 0
1
vote
7
replies
1.9k
views
Adding geneID to list of gene locus IDs
cluster OrgDb clusterProfiler
written 2.1 years ago by • 0
0
votes
4
replies
1.9k
views
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
OrgDb
24 months ago hendrikwenneker • 0
1
vote
9
replies
2.0k
views
Why is OrgDb linked to specific biocversion? / How to analyze old datasets?
BiocVersion OrgDb clusterProfiler
2.1 years ago MK • 0
0
votes
1
reply
878
views
Share Annotation Packages
OrgDb AnnotationDbi
updated 2.2 years ago by 4.1k • written 2.2 years ago by • 0
0
votes
1
reply
1.5k
views
Exporting org.*.*.db Gene Ontology annotations to excel sheet or txt
OrgDb RNASeq
updated 2.9 years ago by 67k • written 2.9 years ago by • 0
0
votes
7
replies
5.6k
views
how to create an OrgDb package?
orgDb annotationForge
updated 2.7 years ago by • 0 • written 3.2 years ago by ▴ 20
1
vote
2
replies
1.8k
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb Bioconductor AnnotationHub clusterProfiler
updated 3.6 years ago by ★ 4.1k • written 3.6 years ago by • 0
0
votes
0
replies
1.1k
views
Adding to Pseudomonas aeruginosa PAO1 to OrgDb
OrgDb
3.7 years ago Thomas.H.Hampton • 0
2
votes
3
replies
2.1k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 3.9 years ago by 67k • written 3.9 years ago by ▴ 30
0
votes
2
replies
1.6k
views
Can't select GO from AnnotationHub orgDB packages
GO.db AnnotationHub OrgDB
updated 4.4 years ago by 67k • written 4.4 years ago by ★ 2.0k
3
votes
6
replies
2.8k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 2.4 years ago by 4.1k • written 4.6 years ago by ★ 2.0k
0
votes
34
replies
9.6k
views
Error: installation of package org.Mm.eg.db had non-zero exit status
OrgDb
updated 4.7 years ago by • 0 • written 5.1 years ago by • 0
7
votes
44
replies
6.4k
views
OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 5.4 years ago by 4.1k • written 5.5 years ago by ▴ 10
3
votes
6
replies
2.2k
views
How to create a customized OrgDb in order to perform kegga analysis?
limma kegga orgdb
updated 6.8 years ago by 52k • written 6.8 years ago by • 0
0
votes
1
reply
1.6k
views
News: OrgDbs in AnnotationHub
annotationhub orgdb News
7.1 years ago shepherl 4.1k
0
votes
0
replies
1.5k
views
News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
7.1 years ago shepherl 4.1k
0
votes
6
replies
1.8k
views
Why are important organisms missing from AnnotationHub. Example query(hub, "Zea")
orgdb annotationhub
7.3 years ago slbai01 • 0
0
votes
2
replies
2.3k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
7.4 years ago Didi ▴ 10
1
vote
0
replies
1.3k
views
News: complete set of OrgDb packages have been added to AnnotationHub
bioconductor annotationhub orgdb News
7.5 years ago shepherl 4.1k
0
votes
4
replies
1.5k
views
Annotation Hub object no longer present
Orgdb
8.0 years ago anamabrantesc • 0
2
votes
12
replies
2.6k
views
ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not work well
annotation orgdb
8.8 years ago knishida ▴ 20
3
votes
13
replies
3.0k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub organismdb orgdb unsupported organisms
updated 8.9 years ago by ★ 6.8k • written 8.9 years ago by ★ 4.1k
0
votes
5
replies
2.1k
views
Why are important organisms missing from AnnotationHub() $rdataclass == "OrgDb"?
annotationhub orgdb
updated 9.1 years ago by ★ 6.8k • written 9.1 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Error in makeOrgPackageFromNCBI
GO OrgDb annotate GOstats GO OrgDb annotate GOstats
11.5 years ago Chris Whelan ▴ 60
0
votes
6
replies
1.7k
views
Creating an OrganismDbi package with a few transcript annotations
OrgDb OrganismDbi OrgDb OrganismDbi
updated 11.6 years ago by 25k • written 11.6 years ago by ★ 11k
0
votes
1
reply
1.9k
views
problem creating own org.Ss.eg.db
Annotation GO Organism OrgDb Annotation GO Organism OrgDb
updated 12.8 years ago by ★ 4.1k • written 12.8 years ago by ★ 7.2k
32 results • Page 1 of 1
Recent ...
Replies
Comment: Help using rtracklayer for gene ID extraction by Aichatou • 0
Thank you very much for the quick response. However, I am unable to reproduce the code you provided. It starts to run, then I get the error…
Answer: Deseq2 Design by James W. MacDonald 67k
Trying to use a conventional factor analysis, particularly if you are new, is not the way to go (I have been doing this for over 20 years n…
Answer: p value is 0, padj is 0 by swbarnes2 ★ 1.4k
I think the default smallest value R will return is 1x10^-300. So I'd take a look at the counts, and see if it makes sense that the p-valu…
Comment: p value is 0, padj is 0 by Michael Love 43k
``` > set.seed(1); t.test(rnorm(200,rep(c(0,80),each=100)) ~ rep(0:1,each=100))$p.value [1] 0 ```
Answer: Cannot install GO.db and org.Hs.eg.db by James W. MacDonald 67k
You might try tracing the namespace loading. ``` Sys.setenv("_R_TRACE_LOADNAMESPACE_"="2") install("org.Hs.eg.db") ``` And see if th…
Votes
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
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