Showing : AnnotationForge • reset
2
votes
28
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4.5k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 5 months ago by 66k • written 17 months ago by ▴ 10
5
votes
22
replies
5.5k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 7.9 years ago by ★ 1.0k • written 9.3 years ago by • 0
1
vote
22
replies
4.7k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor R annotationforge
updated 7.4 years ago by ▴ 10 • written 7.8 years ago by • 0
1
vote
15
replies
2.3k
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
15 months ago • updated 14 months ago Mistinrain ▴ 10
0
votes
14
replies
4.9k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
7.3 years ago • updated 21 months ago Jenny Drnevich ★ 2.0k
0
votes
12
replies
5.4k
views
Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Microarray GO oligo AnnotationForge Microarray GO oligo AnnotationForge
11.3 years ago James W. MacDonald 66k
0
votes
10
replies
1.5k
views
Error during makeOrgPackageFromNCBI
annotationforge makeorgpackagefromncbi
6.9 years ago gabciamm • 0
3
votes
9
replies
2.9k
views
Create object "Go3AnnDbBimap" and include it in a org.Xx.eg.db package to use with goProfiles and goTools
goprofiles AnnotationForge Bimap GO
9.7 years ago artur ▴ 80
3
votes
8
replies
2.6k
views
AnnotationForge::makeOrgPackage GO Ids mistake
AnnotationHubData AnnotationForge
2.1 years ago Saber_J ▴ 10
5
votes
7
replies
1.8k
views
Problem with installing packages made by makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI gene ontology edgeR pathwayanalysis
updated 13 months ago by ▴ 50 • written 4.2 years ago by ▴ 20
1
vote
7
replies
1.4k
views
Error:object 'lookup_tax_id_by_organism' not found with makeOrgPackageFromNCBI
annotationforge
updated 5.7 years ago by 66k • written 5.7 years ago by • 0
3
votes
7
replies
2.6k
views
makeOrgPackage in AnnotationForge "GID" problem
annotationforge
updated 7.1 years ago by 66k • written 7.1 years ago by • 0
0
votes
7
replies
1.8k
views
go_bp table in custom OrgDb package
annotation go pcaExplorer AnnotationForge
updated 5.2 years ago by 66k • written 5.2 years ago by • 0
0
votes
7
replies
4.5k
views
how to create an OrgDb package?
orgDb annotationForge
updated 2.1 years ago by • 0 • written 2.6 years ago by • 0
3
votes
6
replies
1.0k
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge OrganismData OrganismDb
11 months ago abhisek001 • 0
3
votes
6
replies
2.6k
views
RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation microarray annotate annotationforge
7.3 years ago MOD • 0
0
votes
5
replies
2.1k
views
Error during makeOrgPackageFromNCBI
annotation annotationforge annotationdbi makeorgpackagefromncbi
9.3 years ago oliver.tills • 0
1
vote
5
replies
1.4k
views
Gene ID conversion for pathway enrichment analysis of differentially expressed genes
GeneIDConversion AnnotationForge
updated 3.1 years ago by ★ 4.0k • written 3.2 years ago by • 0
2
votes
5
replies
837
views
Help with orgdb for non-model species via makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI
updated 7 months ago by 66k • written 7 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 4.0 years ago by 66k • written 4.0 years ago by • 0
0
votes
5
replies
343
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 4 weeks ago by 66k • written 4 weeks 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 9.7 years ago by ★ 3.7k
2
votes
4
replies
737
views
Question about creating custom organism database with AnnotationForge
AnnotationForge
7 months ago Adrian • 0
0
votes
4
replies
972
views
AnnotationForge not working for building custom org packages
AnnotationForge Marc Carlson Hervé Pagès
updated 4.1 years ago by 66k • written 4.1 years ago by • 0
2
votes
4
replies
1.0k
views
MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI NCBI SQL AnnotationForge
updated 4.0 years ago by 66k • written 4.0 years ago by • 0
1
vote
4
replies
2.7k
views
AnnotationForge failed due to "Parameter 0 does not have length 1"
AnnotationForge
updated 8.4 years ago by ★ 6.8k • written 8.4 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 10.8 years ago by ★ 7.2k • written 10.8 years ago by ▴ 220
1
vote
3
replies
1.1k
views
makeOrgPackageFromNCBI - cannot connect to BioMart
annotationforge
updated 5.8 years ago by 66k • written 5.8 years ago by • 0
2
votes
3
replies
1.8k
views
custom annotation for GO enrichment
annotationforge GSEA clusterprofiler GO annotation
6.8 years ago cabezasdelafuented ▴ 10
3
votes
3
replies
8.7k
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 9.7 years ago by ★ 7.2k • written 9.7 years ago by ▴ 80
0
votes
3
replies
1.3k
views
error while making database using Annotationforge package
annotationforge error database
updated 7.8 years ago by ★ 4.0k • written 7.8 years ago by ▴ 10
1
vote
3
replies
1.4k
views
Running GO analysis via Prostar
prostar proteomics rforproteomics annotationforge
updated 6.0 years ago by ▴ 10 • written 6.0 years ago by ▴ 20
3
votes
3
replies
786
views
AnnotationForge run by three days and do not end
annotation AnnotationForge
4.1 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 3.2 years ago by ★ 3.9k • written 3.2 years ago by • 0
0
votes
3
replies
767
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 16 months ago by 66k • written 16 months ago by • 0
0
votes
2
replies
4.1k
views
Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
biomaRt AnnotationForge
2.0 years ago • updated 24 months ago Lan Anh • 0
0
votes
2
replies
817
views
makeOrgPackage Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name
software error go AnnotationForge AnnotationDbi
updated 4.3 years ago by 66k • written 4.3 years ago by • 0
0
votes
2
replies
1.1k
views
error with downloading NCBI data for makeorgpackagefromNCBI?
annotationforge makeOrgPackageFromNCBI
updated 4.3 years ago by 66k • written 4.3 years ago by • 0
1
vote
2
replies
139
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
9 days ago Patadù ▴ 10
0
votes
2
replies
1.6k
views
Error in makeOrgPackageFromNCBI for Medicago truncatula
annotation annotationforge
updated 8.5 years ago by 25k • written 8.5 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
8.9 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 9.7 years ago by ★ 7.2k • written 9.7 years ago by ▴ 80
4
votes
2
replies
4.2k
views
Install package without updating dependent package
Install AnnotationForge
2.5 years ago 亮 • 0
2
votes
2
replies
1.1k
views
Queries around makeOrgPackageFromNCBI
R software error annotationforge
updated 6.1 years ago by ★ 4.0k • written 6.1 years ago by • 0
0
votes
1
reply
1.2k
views
答复: an error in AnnotationForge
Annotation ChipName annotate affy AnnotationForge Annotation ChipName annotate affy
10.8 years ago joseph ▴ 50
0
votes
1
reply
1.7k
views
nsFilter error in genefilter
GO hgu133plus2 cdf GSVA AnnotationForge GO hgu133plus2 cdf GSVA AnnotationForge
updated 10.9 years ago by 66k • written 10.9 years ago by ▴ 90
1
vote
1
reply
541
views
AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
AnnotationForge
16 months ago Mistinrain ▴ 10
0
votes
1
reply
1.8k
views
AnnotationForge makeOrgPackage rsqlite_send_query error
annotationforge makeorgpackage
6.9 years ago marisa.e.miller • 0
0
votes
1
reply
1.4k
views
AnnotationForge, RNAseq, and non-model organism
AnnotationForge annotationforge nonmodel rnaseq
updated 6.4 years ago by 66k • written 6.4 years ago by • 0
0
votes
1
reply
500
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
updated 15 months ago by • 0 • written 15 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Answer: GSVA function by Robert Castelo ★ 3.3k
Hi, We recommend to input normalized expression values in logarithmic scale to GSVA. We also recommend to use the latest release of the …
Comment: Cannot install oligo on Fedora by Guido Hooiveld ★ 4.0k
Aha, that is a good one! Starting from release 40, as I just found out, Fedora apparently is not including/using `zlib` as such anymore, b…
Votes
Answer: How to run allelic imbalance in apeglm
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
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