Showing : organismdb • reset
4
votes
14
replies
2.6k
views
Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() from AnnotationForge
OrganismDb AnnotationForge
17 months ago • updated 16 months ago Ozan • 0
0
votes
3
replies
2.5k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 23 months ago by ★ 4.1k • written 23 months ago by • 0
4
votes
6
replies
2.0k
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge OrganismData OrganismDb
2.4 years ago abhisek001 • 0
1
vote
2
replies
1.6k
views
annotation: how to use "character" for function 'select()'
annotation organismdb
updated 9.2 years ago by 25k • written 9.2 years ago by ★ 4.1k
3
votes
13
replies
3.7k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub organismdb orgdb unsupported organisms
updated 9.8 years ago by ★ 6.8k • written 9.8 years ago by ★ 4.1k
2
votes
2
replies
3.6k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter granges refseq ucsc organismdb
updated 9.9 years ago by ★ 3.4k • written 9.9 years ago by ▴ 10
4
votes
3
replies
3.0k
views
ggbio error: Objects of type OrganismDb not supported by autoplot
GO OrganismDb ggbio GO OrganismDb ggbio
updated 10.9 years ago by ▴ 50 • written 11.2 years ago by ▴ 120
1
vote
2
replies
4.4k
views
Error attaching org.Hs.eg.db package
annotationdbi annotation organismdb loadnamespace
11.0 years ago milorobertsmith • 0
2
votes
2
replies
1.6k
views
How to remove IEA genes from list of GO terms?
go annotation organismdb
updated 11.0 years ago by 68k • written 11.0 years ago by ★ 4.1k
1
vote
2
replies
2.7k
views
AnnotationForge: org.Xx.eg.db created with makeOrgPackage() is missing org.Xx.egGO object.
organismdb annotationdbi annotationforge
updated 11.1 years ago by ★ 7.2k • written 11.1 years ago by ▴ 80
0
votes
1
reply
5.8k
views
Question about MEDIPS extend parameter : RE: Success: RE: Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome MEDIPS
updated 11.9 years ago by ▴ 280 • written 11.9 years ago by 16k
0
votes
0
replies
2.3k
views
Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome GO
11.9 years ago Hervé Pagès 16k
0
votes
0
replies
2.4k
views
BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome rtracklayer MEDIPS
11.9 years ago Hervé Pagès 16k
13 results • Page 1 of 1
Recent ...
Replies
Answer: Integration: Paired-end vs healthy single-end from a different source by James W. MacDonald 68k
If by reprocess you mean generate libraries and re-sequence, then that's something you could do. Otherwise the biological and technical dif…
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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