Showing : org.Mm.eg.db • reset
3
votes
9
replies
2.7k
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 12 months ago by • 0 • written 13 months ago by • 0
1
vote
8
replies
1.8k
views
Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
gsea mice org.Mm.eg.db
updated 15 months ago by 68k • written 16 months ago by • 0
1
vote
9
replies
4.1k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 20 months ago by 68k • written 20 months ago by ▴ 10
3
votes
2
replies
3.3k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 2.5 years ago by ★ 4.1k • written 2.5 years ago by ▴ 10
1
vote
4
replies
3.5k
views
Large differences in gene content for GO terms between org.Mm.eg.db and msigdbr
org.Mm.eg.db GO msigdbr
3.0 years ago S ▴ 10
1
vote
2
replies
1.5k
views
select with org.Mm.eg.db does not give ENSEMBL ids
org.Mm.eg.db
3.1 years ago raf4 ▴ 30
0
votes
1
reply
2.5k
views
Converting gene symbols to entrez ID
AnnotationDbi org.Mm.eg.db
updated 3.9 years ago by 68k • written 3.9 years ago by • 0
1
vote
2
replies
2.6k
views
Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db.
org.Mm.eg.db AnnotationDbi
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 30
0
votes
1
reply
1.5k
views
ENSEMBL records not complete in org.Mm.eg.db?
org.Mm.eg.db
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by • 0
0
votes
2
replies
4.2k
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 4.8 years ago by ★ 4.1k • written 4.8 years ago by • 0
4
votes
5
replies
3.8k
views
Failed to load "org.Mm.eg.db" package
org.Mm.eg.db
4.8 years ago Nicol • 0
2
votes
2
replies
2.8k
views
Error: package or namespace load failed for ‘org.Mm.eg.db':
org.Mm.eg.db
4.8 years ago Jack • 0
0
votes
1
reply
3.4k
views
Download of package ‘org.Mm.eg.db’ failed
org.Mm.eg.db
4.9 years ago kevin • 0
0
votes
4
replies
5.1k
views
Problem with install installation("org.Hs.eg.db") package
org.Mm.eg.db org.Hs.eg.db
4.9 years ago Eslam • 0
1
vote
5
replies
4.7k
views
Is org.Mm.eg.db updated to mus musculus version 99?
org.Mm.eg.db AnnotationDbi
5.8 years ago kavator ▴ 30
2
votes
3
replies
3.5k
views
org.Mm.eg.db gives wrong symbol for MT genes
org.mm.eg.db
12.5 years ago • updated 7.5 years ago Gordon Smyth 53k
1
vote
2
replies
2.2k
views
SYMBOL is not the official MGI gene symbol?
org.mm.eg.db annotationdbi
updated 7.5 years ago by 68k • written 7.5 years ago by ▴ 20
4
votes
3
replies
2.4k
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
7.9 years ago pvd2107 ▴ 30
2
votes
1
reply
1.6k
views
TopGO - Incorrect mapping genes to GO terms
topgo go org.mm.eg.db
updated 8.0 years ago by 68k • written 8.0 years ago by • 0
4
votes
8
replies
6.2k
views
Annotating DEseq output using AnnotationDbi mapIds and most results say NA
AnnotationDbi mapIds org.Mm.eg.db ENSEMBLTRANS
updated 9.1 years ago by 68k • written 9.1 years ago by ▴ 10
1
vote
2
replies
1.6k
views
GO evidence code IMR
org.mm.eg.db GO
9.5 years ago Peter Langfelder ★ 3.0k
0
votes
4
replies
2.1k
views
missing gene_ids in org.Mm.egENSEMBL
org.mm.eg.db annotation
updated 10.2 years ago by 68k • written 10.2 years ago by ▴ 30
7
votes
11
replies
6.6k
views
annotatePeak() in ChIPseeker - how long does it take to run?
annotatePeak chipseeker chipseq org.Mm.eg.db TxDb.Mmusculus.UCSC.mm9.knownGene
updated 10.4 years ago by 25k • written 10.6 years ago by • 0
4
votes
2
replies
4.6k
views
select keys from org.Mm.eg.db
org.mm.eg.db select list
updated 10.4 years ago by 68k • written 10.4 years ago by ★ 1.5k
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 10.5 years ago by • 0 • written 10.7 years ago by • 0
3
votes
2
replies
2.3k
views
Annotating RNAseq with GO (gene ontology) returns #NA for (nearly) all Entrez ids.
org.mm.eg.db annotation rnaseqgene
updated 10.6 years ago by 68k • written 10.6 years ago by • 0
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
10.8 years ago Patrick Schorderet ▴ 20
1
vote
3
replies
2.1k
views
Genome side annotation for drosophila
genome annotation drosophila melanogaster org.Mm.eg.db
updated 10.9 years ago by ★ 7.2k • written 10.9 years ago by ▴ 20
8
votes
4
replies
5.7k
views
how to extract "Gene type" from org.Mm.eg.db?
annotation org.Mm.eg.db
11.2 years ago Guido Hooiveld ★ 4.1k
29 results • Page 1 of 1
Recent ...
Replies
Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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