Showing : AnnotationForge • reset
2
votes
28
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4.3k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 4 months ago by 65k • written 16 months ago by ▴ 10
5
votes
22
replies
5.5k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 7.8 years ago by ★ 1.0k • written 9.2 years ago by • 0
1
vote
22
replies
4.6k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor R annotationforge
updated 7.3 years ago by ▴ 10 • written 7.7 years ago by • 0
1
vote
15
replies
2.1k
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
14 months ago • updated 13 months ago Mistinrain ▴ 10
0
votes
14
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4.8k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
7.2 years ago • updated 20 months ago Jenny Drnevich ★ 2.0k
0
votes
12
replies
5.2k
views
Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Microarray GO oligo AnnotationForge Microarray GO oligo AnnotationForge
11.2 years ago James W. MacDonald 65k
0
votes
10
replies
1.4k
views
Error during makeOrgPackageFromNCBI
annotationforge makeorgpackagefromncbi
6.8 years ago gabciamm • 0
3
votes
9
replies
2.8k
views
Create object "Go3AnnDbBimap" and include it in a org.Xx.eg.db package to use with goProfiles and goTools
goprofiles AnnotationForge Bimap GO
9.6 years ago artur ▴ 80
3
votes
8
replies
2.5k
views
AnnotationForge::makeOrgPackage GO Ids mistake
AnnotationHubData AnnotationForge
24 months ago Saber_J ▴ 10
5
votes
7
replies
1.7k
views
Problem with installing packages made by makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI gene ontology edgeR pathwayanalysis
updated 12 months ago by ▴ 50 • written 4.1 years ago by ▴ 20
3
votes
7
replies
2.5k
views
makeOrgPackage in AnnotationForge "GID" problem
annotationforge
updated 7.0 years ago by 65k • written 7.0 years ago by • 0
0
votes
7
replies
1.7k
views
go_bp table in custom OrgDb package
annotation go pcaExplorer AnnotationForge
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
1
vote
7
replies
1.3k
views
Error:object 'lookup_tax_id_by_organism' not found with makeOrgPackageFromNCBI
annotationforge
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
0
votes
7
replies
4.3k
views
how to create an OrgDb package?
orgDb annotationForge
updated 2.0 years ago by • 0 • written 2.5 years ago by • 0
3
votes
6
replies
2.6k
views
RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation microarray annotate annotationforge
7.2 years ago MOD • 0
3
votes
6
replies
932
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge OrganismData OrganismDb
9 months ago abhisek001 • 0
1
vote
5
replies
1.4k
views
Gene ID conversion for pathway enrichment analysis of differentially expressed genes
GeneIDConversion AnnotationForge
updated 3.0 years ago by ★ 3.9k • written 3.1 years ago by • 0
2
votes
5
replies
735
views
Help with orgdb for non-model species via makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI
updated 6 months ago by 65k • written 6 months ago by ▴ 70
4
votes
5
replies
1.9k
views
makeOrgPackage - ERROR: Two fields in the source DB have the same name
software error AnnotationForge AnnotationDbi
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
0
votes
5
replies
2.0k
views
Error during makeOrgPackageFromNCBI
annotation annotationforge annotationdbi makeorgpackagefromncbi
9.2 years ago oliver.tills • 0
0
votes
4
replies
913
views
AnnotationForge not working for building custom org packages
AnnotationForge Marc Carlson Hervé Pagès
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
2
votes
4
replies
981
views
MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI NCBI SQL AnnotationForge
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
0
votes
4
replies
2.3k
views
IlluminaHumanMethylation450k.db has undeclared dependency on AnnotationForge
annotationforge
updated 9.6 years ago by ★ 7.2k • written 9.6 years ago by ★ 3.7k
1
vote
4
replies
2.7k
views
AnnotationForge failed due to "Parameter 0 does not have length 1"
AnnotationForge
updated 8.3 years ago by ★ 6.8k • written 8.3 years ago by • 0
2
votes
4
replies
660
views
Question about creating custom organism database with AnnotationForge
AnnotationForge
6 months ago Adrian • 0
0
votes
3
replies
1.3k
views
error while making database using Annotationforge package
annotationforge error database
updated 7.7 years ago by ★ 3.9k • written 7.8 years ago by ▴ 10
1
vote
3
replies
1.1k
views
makeOrgPackageFromNCBI - cannot connect to BioMart
annotationforge
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
1
vote
3
replies
1.7k
views
Bug in makeOrgPackageFromNCBI from AnnotationForge?
Alignment Annotation Organism Schizosaccharomyces pombe biomaRt AnnotationForge Alignment
updated 10.6 years ago by ★ 7.2k • written 10.7 years ago by ▴ 220
3
votes
3
replies
8.6k
views
error: "'names' attribute [16] must be the same length as the vector [2]", using Making Organism packages use of makeOrgPackage()
annotationforge Annotation GO
updated 9.6 years ago by ★ 7.2k • written 9.6 years ago by ▴ 80
2
votes
3
replies
1.7k
views
custom annotation for GO enrichment
annotationforge GSEA clusterprofiler GO annotation
6.7 years ago cabezasdelafuented ▴ 10
1
vote
3
replies
1.3k
views
Running GO analysis via Prostar
prostar proteomics rforproteomics annotationforge
updated 5.9 years ago by ▴ 10 • written 5.9 years ago by ▴ 20
3
votes
3
replies
742
views
AnnotationForge run by three days and do not end
annotation AnnotationForge
4.0 years ago Marcelo Laia ▴ 450
0
votes
3
replies
1.3k
views
AnnotationForge: makeOrgPackageFromNCBI Error in function (type, msg, asError = TRUE) : FTP response timeout
AnnotationForge
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
0
votes
3
replies
731
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 15 months ago by 65k • written 15 months ago by • 0
2
votes
2
replies
1.1k
views
Queries around makeOrgPackageFromNCBI
R software error annotationforge
updated 6.0 years ago by ★ 3.9k • written 6.0 years ago by • 0
0
votes
2
replies
789
views
makeOrgPackage Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name
software error go AnnotationForge AnnotationDbi
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
0
votes
2
replies
4.0k
views
Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
biomaRt AnnotationForge
23 months ago Lan Anh • 0
0
votes
2
replies
1.6k
views
Error in makeOrgPackageFromNCBI for Medicago truncatula
annotation annotationforge
updated 8.4 years ago by 25k • written 8.4 years ago by • 0
0
votes
2
replies
1.2k
views
makeOrgPackage: possible to add option to allow GO terms now in GO.db?
annotationforge makeorgpackage go
8.8 years ago Keith Hughitt ▴ 180
1
vote
2
replies
2.1k
views
AnnotationForge: org.Xx.eg.db created with makeOrgPackage() is missing org.Xx.egGO object.
organismdb annotationdbi annotationforge
updated 9.6 years ago by ★ 7.2k • written 9.6 years ago by ▴ 80
0
votes
2
replies
1.1k
views
error with downloading NCBI data for makeorgpackagefromNCBI?
annotationforge makeOrgPackageFromNCBI
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
4
votes
2
replies
4.0k
views
Install package without updating dependent package
Install AnnotationForge
2.4 years ago 亮 • 0
0
votes
1
reply
990
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 12 months ago by 3.8k • written 12 months ago by • 0
0
votes
1
reply
1.7k
views
nsFilter error in genefilter
GO hgu133plus2 cdf GSVA AnnotationForge GO hgu133plus2 cdf GSVA AnnotationForge
updated 10.8 years ago by 65k • written 10.8 years ago by ▴ 90
0
votes
1
reply
1.1k
views
答复: an error in AnnotationForge
Annotation ChipName annotate affy AnnotationForge Annotation ChipName annotate affy
10.7 years ago joseph ▴ 50
0
votes
1
reply
1.0k
views
an error in AnnotationForge
Annotation ChipName annotate affy AnnotationForge Annotation ChipName annotate affy
updated 10.7 years ago by ★ 7.2k • written 10.7 years ago by ▴ 50
1
vote
1
reply
504
views
AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
AnnotationForge
14 months ago Mistinrain ▴ 10
0
votes
1
reply
1.3k
views
AnnotationForge, RNAseq, and non-model organism
AnnotationForge annotationforge nonmodel rnaseq
updated 6.3 years ago by 65k • written 6.3 years ago by • 0
0
votes
1
reply
1.8k
views
AnnotationForge makeOrgPackage rsqlite_send_query error
annotationforge makeorgpackage
6.8 years ago marisa.e.miller • 0
1
vote
1
reply
1.8k
views
Mapping Affymetrix annotations with Bioconductor annotations
Annotation Organism zebrafish cdf affy AnnotationForge Annotation Organism zebrafish cdf
updated 10.5 years ago by 65k • written 10.5 years ago by ▴ 80
50 results • Page 1 of 1
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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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