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org.Mm.eg.db
•
reset
8
votes
4
replies
4.7k
views
how to extract "Gene type" from org.Mm.eg.db?
annotation
org.Mm.eg.db
9.4 years ago
Guido Hooiveld
★ 3.9k
7
votes
11
replies
4.9k
views
annotatePeak() in ChIPseeker - how long does it take to run?
annotatePeak
chipseeker
chipseq
org.Mm.eg.db
TxDb.Mmusculus.UCSC.mm9.knownGene
updated 8.6 years ago by
Martin Morgan
25k • written 8.8 years ago by
Elsa
• 0
4
votes
2
replies
3.4k
views
select keys from org.Mm.eg.db
org.mm.eg.db
select
list
updated 8.6 years ago by
James W. MacDonald
65k • written 8.6 years ago by
Assa Yeroslaviz
★ 1.5k
4
votes
8
replies
4.5k
views
Annotating DEseq output using AnnotationDbi mapIds and most results say NA
AnnotationDbi
mapIds
org.Mm.eg.db
ENSEMBLTRANS
updated 7.3 years ago by
James W. MacDonald
65k • written 7.3 years ago by
Mike
▴ 10
4
votes
3
replies
1.6k
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
6.1 years ago
pvd2107
▴ 30
4
votes
5
replies
2.2k
views
Failed to load "org.Mm.eg.db" package
org.Mm.eg.db
3.1 years ago • updated 3.0 years ago
Nicol
• 0
3
votes
2
replies
1.1k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 8 months ago by
Guido Hooiveld
★ 3.9k • written 8 months ago by
Milan
▴ 10
3
votes
2
replies
1.8k
views
Annotating RNAseq with GO (gene ontology) returns #NA for (nearly) all Entrez ids.
org.mm.eg.db
annotation
rnaseqgene
updated 8.8 years ago by
James W. MacDonald
65k • written 8.8 years ago by
michael.willcockson
• 0
2
votes
2
replies
1.8k
views
Error: package or namespace load failed for ‘org.Mm.eg.db':
org.Mm.eg.db
3.1 years ago
Jack
• 0
2
votes
1
reply
1.2k
views
TopGO - Incorrect mapping genes to GO terms
topgo
go
org.mm.eg.db
updated 6.2 years ago by
James W. MacDonald
65k • written 6.2 years ago by
lehallib
• 0
2
votes
3
replies
2.5k
views
org.Mm.eg.db gives wrong symbol for MT genes
org.mm.eg.db
10.7 years ago • updated 5.7 years ago
Gordon Smyth
50k
1
vote
2
replies
631
views
select with org.Mm.eg.db does not give ENSEMBL ids
org.Mm.eg.db
15 months ago
raf4
▴ 20
1
vote
3
replies
1.4k
views
Genome side annotation for drosophila
genome annotation
drosophila melanogaster
org.Mm.eg.db
updated 9.1 years ago by
Marc Carlson
★ 7.2k • written 9.1 years ago by
Patrick Schorderet
▴ 20
1
vote
2
replies
11k
views
select() gene in db not working although key exists
annotationdbi
org.mm.eg.db
org.dm.eg.db
select
9.1 years ago
Patrick Schorderet
▴ 20
1
vote
2
replies
1.2k
views
GO evidence code IMR
org.mm.eg.db
GO
7.8 years ago
Peter Langfelder
★ 3.0k
1
vote
2
replies
1.3k
views
SYMBOL is not the official MGI gene symbol?
org.mm.eg.db
annotationdbi
updated 5.7 years ago by
James W. MacDonald
65k • written 5.7 years ago by
brendan.innes
▴ 20
1
vote
5
replies
2.5k
views
Is org.Mm.eg.db updated to mus musculus version 99?
org.Mm.eg.db
AnnotationDbi
4.0 years ago
kavator
▴ 30
1
vote
4
replies
1.2k
views
Large differences in gene content for GO terms between org.Mm.eg.db and msigdbr
org.Mm.eg.db
GO
msigdbr
14 months ago
S
▴ 10
1
vote
2
replies
1.5k
views
Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db.
org.Mm.eg.db
AnnotationDbi
updated 2.8 years ago by
James W. MacDonald
65k • written 2.8 years ago by
abf
▴ 30
0
votes
1
reply
2.4k
views
How to use org.Mm.eg.db as chip in topGO printGenes function
topgo
org.mm.eg.db
updated 8.8 years ago by
fletchkatie
• 0 • written 8.9 years ago by
komalr
• 0
0
votes
2
replies
2.6k
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 3.0 years ago by
Guido Hooiveld
★ 3.9k • written 3.0 years ago by
1627166123
• 0
0
votes
1
reply
1.5k
views
Converting gene symbols to entrez ID
AnnotationDbi
org.Mm.eg.db
updated 2.1 years ago by
James W. MacDonald
65k • written 2.1 years ago by
rl19
• 0
0
votes
4
replies
3.7k
views
Problem with install installation("org.Hs.eg.db") package
org.Mm.eg.db
org.Hs.eg.db
3.2 years ago • updated 3.1 years ago
Eslam
• 0
0
votes
1
reply
868
views
ENSEMBL records not complete in org.Mm.eg.db?
org.Mm.eg.db
updated 3.0 years ago by
Kevin Blighe
★ 3.9k • written 3.0 years ago by
Ming Wang
• 0
0
votes
1
reply
1.6k
views
Download of package ‘org.Mm.eg.db’ failed
org.Mm.eg.db
3.2 years ago
kevin
• 0
0
votes
4
replies
1.5k
views
missing gene_ids in org.Mm.egENSEMBL
org.mm.eg.db
annotation
updated 8.4 years ago by
James W. MacDonald
65k • written 8.4 years ago by
Gregulator
▴ 30
26 results • Page
1 of 1
Recent ...
Replies
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Comment: Help with running egsea()
by
James W. MacDonald
65k
I don't understand the last question, but do look at the msigdb.gsets argument to `buildIdx` in the help page for that function.
Answer: Help with running egsea()
by
James W. MacDonald
65k
There are no arguments to `egsea.base`, as it is meant only as a helper function to return the different methods. In addition, if you are u…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I am working with mouse data. I don't know how to do this, but I will go through it. Can you help me with the second question? how do we …
Comment: [Mfuzz] Error in cmeans(exprs(eset)
by
Caio
• 0
You can have this problem (lines with variance equal to zero) when you run experiments and obtain the data with more samples and use fewer …
Votes
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Answer: How to save the DEXSeq results
Answer: Help with running egsea()
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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