Showing : organismdb • reset
4
votes
14
replies
2.6k
views
Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() from AnnotationForge
OrganismDb AnnotationForge
16 months ago Ozan • 0
0
votes
3
replies
2.4k
views
How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 22 months ago by ★ 4.1k • written 22 months ago by • 0
4
votes
6
replies
1.9k
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge OrganismData OrganismDb
2.3 years ago abhisek001 • 0
1
vote
2
replies
1.6k
views
annotation: how to use "character" for function 'select()'
annotation organismdb
updated 9.1 years ago by 25k • written 9.1 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 9.7 years ago by ★ 6.8k • written 9.7 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
10.9 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
5.7k
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 11.8 years ago by ▴ 280 • written 11.8 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
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Answer: DESeq2 design for haplotype MPRA by Michael Love 43k
> My goal is to identify which non-reference haplotypes are differentially active compared to the corresponding ref/ref haplotype within ea…
Answer: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
It seems fine on devel as well. ``` > BSgenome.Hsapiens.UCSC.hg38 | BSgenome object for Human | - organism: Homo sapiens | - provide…
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
R-4.5.1 is compatible with both release and devel versions of Bioconductor. Which one are you using? I am still on release, and it's fine: …
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by umairmugal82 • 0
When accuracy matters in academic assessment, nothing should be left to chance. [Accurate grading made simple on EasyGrader.net][1] ensures…
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Votes
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
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