Showing : OrgDb • reset
7
votes
44
replies
5.4k
views
OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 4.8 years ago by 3.8k • written 4.8 years ago by • 0
0
votes
34
replies
8.3k
views
Error: installation of package org.Mm.eg.db had non-zero exit status
OrgDb
updated 4.0 years ago by • 0 • written 4.5 years ago by • 0
3
votes
13
replies
2.6k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub organismdb orgdb unsupported organisms
updated 8.2 years ago by ★ 6.8k • written 8.2 years ago by ★ 3.9k
2
votes
12
replies
2.3k
views
ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not work well
annotation orgdb
8.2 years ago knishida ▴ 20
1
vote
9
replies
1.5k
views
Why is OrgDb linked to specific biocversion? / How to analyze old datasets?
BiocVersion OrgDb clusterProfiler
17 months ago MK • 0
0
votes
7
replies
4.3k
views
how to create an OrgDb package?
orgDb annotationForge
updated 2.0 years ago by • 0 • written 2.5 years ago by • 0
1
vote
7
replies
1.4k
views
Adding geneID to list of gene locus IDs
cluster OrgDb clusterProfiler
written 17 months ago by • 0
0
votes
6
replies
1.6k
views
Why are important organisms missing from AnnotationHub. Example query(hub, "Zea")
orgdb annotationhub
6.7 years ago slbai01 • 0
3
votes
6
replies
1.9k
views
How to create a customized OrgDb in order to perform kegga analysis?
limma kegga orgdb
updated 6.2 years ago by 50k • written 6.2 years ago by • 0
0
votes
6
replies
1.5k
views
Creating an OrganismDbi package with a few transcript annotations
OrgDb OrganismDbi OrgDb OrganismDbi
updated 10.9 years ago by 25k • written 10.9 years ago by ★ 11k
3
votes
6
replies
2.2k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 21 months ago by 3.8k • written 3.9 years ago by ★ 2.0k
0
votes
5
replies
1.8k
views
Why are important organisms missing from AnnotationHub() $rdataclass == "OrgDb"?
annotationhub orgdb
updated 8.4 years ago by ★ 6.8k • written 8.4 years ago by ▴ 10
0
votes
4
replies
1.3k
views
Annotation Hub object no longer present
Orgdb
7.4 years ago anamabrantesc • 0
0
votes
4
replies
1.3k
views
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
OrgDb
16 months ago hendrikwenneker • 0
2
votes
4
replies
500
views
Need help generating BSgenome and orgdb
OrgDb BSgenome
5 months ago • updated 10 weeks ago mat149 ▴ 70
2
votes
3
replies
1.7k
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
1
vote
3
replies
439
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo OrgDb convert Organismname RStudio
updated 5 months ago by 65k • written 5 months ago by • 0
1
vote
2
replies
1.4k
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb Bioconductor AnnotationHub clusterProfiler
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
0
votes
2
replies
2.0k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
6.7 years ago Didi ▴ 10
0
votes
2
replies
1.3k
views
Can't select GO from AnnotationHub orgDB packages
GO.db AnnotationHub OrgDB
updated 3.7 years ago by 65k • written 3.7 years ago by ★ 2.0k
0
votes
1
reply
669
views
Share Annotation Packages
OrgDb AnnotationDbi
updated 18 months ago by 3.8k • written 18 months ago by • 0
0
votes
1
reply
1.6k
views
problem creating own org.Ss.eg.db
Annotation GO Organism OrgDb Annotation GO Organism OrgDb
updated 12.1 years ago by ★ 3.9k • written 12.1 years ago by ★ 7.2k
0
votes
1
reply
1.4k
views
News: OrgDbs in AnnotationHub
annotationhub orgdb News
6.4 years ago shepherl 3.8k
2
votes
1
reply
175
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 25 days ago by ★ 3.9k • written 27 days ago by ▴ 10
1
vote
1
reply
46
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 13 hours ago by ★ 3.9k • written 14 hours ago by • 0
0
votes
1
reply
1.2k
views
Exporting org.*.*.db Gene Ontology annotations to excel sheet or txt
OrgDb RNASeq
updated 2.2 years ago by 65k • written 2.2 years ago by • 0
0
votes
0
replies
821
views
Adding to Pseudomonas aeruginosa PAO1 to OrgDb
OrgDb
3.0 years ago Thomas.H.Hampton • 0
0
votes
0
replies
1.3k
views
News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
6.5 years ago shepherl 3.8k
1
vote
0
replies
1.1k
views
News: complete set of OrgDb packages have been added to AnnotationHub
bioconductor annotationhub orgdb News
6.9 years ago shepherl 3.8k
0
votes
0
replies
1.6k
views
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
OrgDb
15 months ago hswdl • 0
0
votes
0
replies
1.3k
views
Error in makeOrgPackageFromNCBI
GO OrgDb annotate GOstats GO OrgDb annotate GOstats
10.9 years ago Chris Whelan ▴ 60
31 results • Page 1 of 1
Recent ...
Replies
Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts by Michael Love 41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts by Michael Love 41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data by normawiedman059 • 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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