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Showing :
OrgDb
•
reset
2
votes
12
replies
2.7k
views
ann_objs$MAPCOUNTS <- AnnotationDbi:::createMAPCOUNTS(dbconn, prefix) does not work well
annotation
orgdb
9.0 years ago
knishida
▴ 20
1
vote
7
replies
2.0k
views
Adding geneID to list of gene locus IDs
cluster
OrgDb
clusterProfiler
written 2.2 years ago by
Chruut
• 0
0
votes
4
replies
2.1k
views
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
OrgDb
2.2 years ago
hendrikwenneker
• 0
0
votes
4
replies
1.6k
views
Annotation Hub object no longer present
Orgdb
8.2 years ago
anamabrantesc
• 0
7
votes
44
replies
6.7k
views
OrgDB download failed via AnnotationHub
annotationhub
orgdb
updated 5.6 years ago by
shepherl
4.1k • written 5.7 years ago by
chirag.parsania
▴ 10
3
votes
6
replies
2.9k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub
OrgDb
snapshotDate
updated 2.6 years ago by
shepherl
4.1k • written 4.7 years ago by
Jenny Drnevich
★ 2.0k
2
votes
2
replies
907
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
sansan
• 0
0
votes
2
replies
2.3k
views
add annotation features to BSgenome or txdb package
bsgenome
txdb
annotation
orgdb
7.6 years ago • updated 7.5 years ago
Didi
▴ 10
3
votes
6
replies
2.3k
views
How to create a customized OrgDb in order to perform kegga analysis?
limma
kegga
orgdb
updated 7.0 years ago by
Gordon Smyth
52k • written 7.0 years ago by
baus87
• 0
0
votes
34
replies
9.9k
views
Error: installation of package org.Mm.eg.db had non-zero exit status
OrgDb
updated 4.8 years ago by
Michaël Degaud
• 0 • written 5.3 years ago by
zhangdengwei
• 0
2
votes
3
replies
2.2k
views
Gene Ontology Analysis of DE Genes
clusterProfiler
AnnotationDbi
OrgDb
goseq
updated 4.0 years ago by
James W. MacDonald
68k • written 4.0 years ago by
vanbelj
▴ 30
1
vote
9
replies
2.2k
views
Why is OrgDb linked to specific biocversion? / How to analyze old datasets?
BiocVersion
OrgDb
clusterProfiler
2.3 years ago
MK
• 0
1
vote
2
replies
1.9k
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb
Bioconductor
AnnotationHub
clusterProfiler
updated 3.8 years ago by
Guido Hooiveld
★ 4.1k • written 3.8 years ago by
ju.ry
• 0
1
vote
3
replies
790
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo
OrgDb
convert
Organismname
RStudio
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
j_denton
• 0
0
votes
6
replies
1.7k
views
Creating an OrganismDbi package with a few transcript annotations
OrgDb
OrganismDbi
OrgDb
OrganismDbi
updated 11.7 years ago by
Martin Morgan
25k • written 11.7 years ago by
Michael Lawrence
★ 11k
0
votes
7
replies
5.9k
views
how to create an OrgDb package?
orgDb
annotationForge
updated 2.8 years ago by
pengxinyang12
• 0 • written 3.3 years ago by
Haibo Liu
▴ 20
0
votes
5
replies
2.1k
views
Why are important organisms missing from AnnotationHub() $rdataclass == "OrgDb"?
annotationhub
orgdb
updated 9.2 years ago by
Valerie Obenchain
★ 6.8k • written 9.2 years ago by
efoss
▴ 10
0
votes
1
reply
1.6k
views
Exporting org.*.*.db Gene Ontology annotations to excel sheet or txt
OrgDb
RNASeq
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
Jonas
• 0
2
votes
4
replies
981
views
Need help generating BSgenome and orgdb
OrgDb
BSgenome
15 months ago • updated 12 months ago
mat149
▴ 80
3
votes
13
replies
3.2k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub
organismdb
orgdb
unsupported organisms
updated 9.0 years ago by
Valerie Obenchain
★ 6.8k • written 9.1 years ago by
Guido Hooiveld
★ 4.1k
1
vote
8
replies
987
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 4 months ago by
James W. MacDonald
68k • written 9 months ago by
Gayatri
• 0
0
votes
2
replies
1.7k
views
Can't select GO from AnnotationHub orgDB packages
GO.db
AnnotationHub
OrgDB
updated 4.6 years ago by
James W. MacDonald
68k • written 4.6 years ago by
Jenny Drnevich
★ 2.0k
0
votes
1
reply
1.9k
views
problem creating own org.Ss.eg.db
Annotation
GO
Organism
OrgDb
Annotation
GO
Organism
OrgDb
updated 13.0 years ago by
Guido Hooiveld
★ 4.1k • written 13.0 years ago by
Marc Carlson
★ 7.2k
0
votes
1
reply
1.6k
views
News:
OrgDbs in AnnotationHub
annotationhub
orgdb
News
7.2 years ago
shepherl
4.1k
0
votes
1
reply
909
views
Share Annotation Packages
OrgDb
AnnotationDbi
updated 2.3 years ago by
shepherl
4.1k • written 2.3 years ago by
Imad
• 0
1
vote
0
replies
1.4k
views
News:
complete set of OrgDb packages have been added to AnnotationHub
bioconductor
annotationhub
orgdb
News
7.7 years ago
shepherl
4.1k
0
votes
6
replies
1.9k
views
Why are important organisms missing from AnnotationHub. Example query(hub, "Zea")
orgdb
annotationhub
7.5 years ago
slbai01
• 0
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
7.3 years ago
shepherl
4.1k
0
votes
0
replies
1.1k
views
Adding to Pseudomonas aeruginosa PAO1 to OrgDb
OrgDb
3.8 years ago
Thomas.H.Hampton
• 0
2
votes
2
replies
906
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
written 10 months ago by
enee
▴ 10
0
votes
0
replies
2.5k
views
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
OrgDb
2.1 years ago
hswdl
• 0
0
votes
0
replies
1.4k
views
Error in makeOrgPackageFromNCBI
GO
OrgDb
annotate
GOstats
GO
OrgDb
annotate
GOstats
11.7 years ago
Chris Whelan
▴ 60
32 results • Page
1 of 1
Recent ...
Replies
Comment: Why the order of sample names in the beta matrix affect the analysis results of
by
81becky
• 0
It sounds like you're experiencing a common issue with data alignment in Champ.DMP. Ensure that your beta matrix and PD files are consisten…
Comment: accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
by
Blair
• 0
@[Sprunki][1] wrote: Please read the vignette and think about adhering to the author's best practice, which discusses batch impacts. [1…
Comment: error in ChAMP loading file
by
81becky
• 0
hi Giulia, it sounds like you're facing a frustating issue with your chAMP import. One common suggestion is to double-check your CSV fomat…
Answer: DESeq2 adujsted p-value cutoff seemingly not working
by
James W. MacDonald
68k
From `?results' ``` On p-values: By default, independent filtering is performed to select a set of genes for multiple tes…
Comment: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode =
by
SofieK
• 0
Thank you, I will try this and see.
Votes
Answer: Efficiently working with HDF5-backed SingleCellExperiments
Efficiently working with HDF5-backed SingleCellExperiments
A: Effect of lfcThreshold on p-value in DESeq2
Answer: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
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