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org.mm.eg.db
•
reset
8
votes
4
replies
5.5k
views
how to extract "Gene type" from org.Mm.eg.db?
annotation
org.Mm.eg.db
11.0 years ago
Guido Hooiveld
★ 4.1k
7
votes
11
replies
6.3k
views
annotatePeak() in ChIPseeker - how long does it take to run?
annotatePeak
chipseeker
chipseq
org.Mm.eg.db
TxDb.Mmusculus.UCSC.mm9.knownGene
updated 10.2 years ago by
Martin Morgan
25k • written 10.4 years ago by
Elsa
• 0
4
votes
3
replies
2.3k
views
Selecting Correct Set of Gene IDs from Mouse Gencode GFF3 for RNA Seq Analysis (Removing Genes without symbols)
deseq2
tximport
org.mm.eg.db
gencode
7.7 years ago
pvd2107
▴ 30
4
votes
5
replies
3.7k
views
Failed to load "org.Mm.eg.db" package
org.Mm.eg.db
4.7 years ago • updated 4.6 years ago
Nicol
• 0
4
votes
2
replies
4.4k
views
select keys from org.Mm.eg.db
org.mm.eg.db
select
list
updated 10.2 years ago by
James W. MacDonald
68k • written 10.2 years ago by
Assa Yeroslaviz
★ 1.5k
4
votes
8
replies
5.9k
views
Annotating DEseq output using AnnotationDbi mapIds and most results say NA
AnnotationDbi
mapIds
org.Mm.eg.db
ENSEMBLTRANS
updated 8.9 years ago by
James W. MacDonald
68k • written 8.9 years ago by
Mike
▴ 10
3
votes
2
replies
2.2k
views
Annotating RNAseq with GO (gene ontology) returns #NA for (nearly) all Entrez ids.
org.mm.eg.db
annotation
rnaseqgene
updated 10.4 years ago by
James W. MacDonald
68k • written 10.4 years ago by
michael.willcockson
• 0
3
votes
9
replies
2.0k
views
Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) returning drastically different numbers of transcripts
AnnotationDbi
EnsDb.Mmusculus.v79
biomaRt
org.Mm.eg.db
updated 10 months ago by
franknappi14
• 0 • written 11 months ago by
Nicholas
• 0
3
votes
2
replies
2.8k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 2.3 years ago by
Guido Hooiveld
★ 4.1k • written 2.3 years ago by
Milan
▴ 10
2
votes
1
reply
1.6k
views
TopGO - Incorrect mapping genes to GO terms
topgo
go
org.mm.eg.db
updated 7.9 years ago by
James W. MacDonald
68k • written 7.9 years ago by
lehallib
• 0
2
votes
2
replies
2.7k
views
Error: package or namespace load failed for ‘org.Mm.eg.db':
org.Mm.eg.db
4.7 years ago
Jack
• 0
2
votes
3
replies
3.3k
views
org.Mm.eg.db gives wrong symbol for MT genes
org.mm.eg.db
12.4 years ago • updated 7.3 years ago
Gordon Smyth
53k
1
vote
8
replies
1.6k
views
Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
gsea
mice
org.Mm.eg.db
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
Gordon
• 0
1
vote
3
replies
2.1k
views
Genome side annotation for drosophila
genome annotation
drosophila melanogaster
org.Mm.eg.db
updated 10.7 years ago by
Marc Carlson
★ 7.2k • written 10.7 years ago by
Patrick Schorderet
▴ 20
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
10.7 years ago
Patrick Schorderet
▴ 20
1
vote
2
replies
1.5k
views
GO evidence code IMR
org.mm.eg.db
GO
9.4 years ago
Peter Langfelder
★ 3.0k
1
vote
2
replies
2.0k
views
SYMBOL is not the official MGI gene symbol?
org.mm.eg.db
annotationdbi
updated 7.3 years ago by
James W. MacDonald
68k • written 7.3 years ago by
brendan.innes
▴ 20
1
vote
5
replies
4.4k
views
Is org.Mm.eg.db updated to mus musculus version 99?
org.Mm.eg.db
AnnotationDbi
5.6 years ago
kavator
▴ 30
1
vote
4
replies
2.7k
views
Large differences in gene content for GO terms between org.Mm.eg.db and msigdbr
org.Mm.eg.db
GO
msigdbr
2.8 years ago
S
▴ 10
1
vote
2
replies
2.4k
views
Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db.
org.Mm.eg.db
AnnotationDbi
updated 4.4 years ago by
James W. MacDonald
68k • written 4.4 years ago by
abf
▴ 30
1
vote
9
replies
3.3k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2
clusterProfiler
Pathways
RNASeq
org.Mm.eg.db
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
adrip
▴ 10
1
vote
2
replies
1.4k
views
select with org.Mm.eg.db does not give ENSEMBL ids
org.Mm.eg.db
2.9 years ago
raf4
▴ 30
0
votes
1
reply
2.3k
views
Converting gene symbols to entrez ID
AnnotationDbi
org.Mm.eg.db
updated 3.7 years ago by
James W. MacDonald
68k • written 3.7 years ago by
rl19
• 0
0
votes
4
replies
4.9k
views
Problem with install installation("org.Hs.eg.db") package
org.Mm.eg.db
org.Hs.eg.db
4.8 years ago
Eslam
• 0
0
votes
1
reply
1.5k
views
ENSEMBL records not complete in org.Mm.eg.db?
org.Mm.eg.db
updated 4.6 years ago by
Kevin Blighe
★ 4.0k • written 4.6 years ago by
Ming Wang
• 0
0
votes
4
replies
2.0k
views
missing gene_ids in org.Mm.egENSEMBL
org.mm.eg.db
annotation
updated 10.0 years ago by
James W. MacDonald
68k • written 10.0 years ago by
Gregulator
▴ 30
0
votes
1
reply
3.2k
views
Download of package ‘org.Mm.eg.db’ failed
org.Mm.eg.db
4.8 years ago
kevin
• 0
0
votes
1
reply
2.8k
views
How to use org.Mm.eg.db as chip in topGO printGenes function
topgo
org.mm.eg.db
updated 10.4 years ago by
fletchkatie
• 0 • written 10.5 years ago by
komalr
• 0
0
votes
2
replies
4.0k
views
Error in testForValidKeytype(x, keytype) : Invalid keytype: TAIR. Please use the keytypes method to see a listing of valid arguments.
org.Mm.eg.db
updated 4.6 years ago by
Guido Hooiveld
★ 4.1k • written 4.6 years ago by
1627166123
• 0
29 results • Page
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Replies
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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Lluís Revilla Sancho
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James W. MacDonald
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shepherl
4.2k
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Gordon Smyth
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