Showing : annotationForge • reset
0
votes
5
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288
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Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 9 days ago by 65k • written 12 days ago by • 0
2
votes
4
replies
714
views
Question about creating custom organism database with AnnotationForge
AnnotationForge
6 months ago Adrian • 0
2
votes
5
replies
784
views
Help with orgdb for non-model species via makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI
updated 6 months ago by 65k • written 6 months ago by ▴ 70
3
votes
6
replies
960
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge OrganismData OrganismDb
10 months ago abhisek001 • 0
0
votes
1
reply
1.1k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 12 months ago by 3.9k • written 12 months ago by • 0
0
votes
1
reply
486
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
updated 15 months ago by • 0 • written 15 months ago by ▴ 10
1
vote
15
replies
2.2k
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
15 months ago • updated 14 months ago Mistinrain ▴ 10
1
vote
1
reply
525
views
AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
AnnotationForge
15 months ago Mistinrain ▴ 10
0
votes
3
replies
754
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
28
replies
4.4k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 5 months ago by 65k • written 17 months ago by ▴ 10
0
votes
2
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4.1k
views
Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
biomaRt AnnotationForge
23 months ago Lan Anh • 0
3
votes
8
replies
2.6k
views
AnnotationForge::makeOrgPackage GO Ids mistake
AnnotationHubData AnnotationForge
2.0 years ago Saber_J ▴ 10
4
votes
2
replies
4.1k
views
Install package without updating dependent package
Install AnnotationForge
2.4 years ago 亮 • 0
0
votes
7
replies
4.3k
views
how to create an OrgDb package?
orgDb annotationForge
updated 2.1 years ago by • 0 • written 2.5 years ago by • 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 ★ 3.9k • written 3.1 years ago by • 0
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
2
votes
4
replies
1.0k
views
MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI NCBI SQL AnnotationForge
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
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 65k • written 4.0 years ago by • 0
3
votes
3
replies
766
views
AnnotationForge run by three days and do not end
annotation AnnotationForge
4.0 years ago Marcelo Laia ▴ 450
1
vote
1
reply
1.3k
views
How to get GOSemSim work on custom packages built with AnnotationForge
Guangchuang Yu GOSemSim AnnotationForge
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
0
votes
4
replies
949
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
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 4.2 years ago by ▴ 20
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
0
votes
2
replies
806
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 65k • written 4.3 years ago by • 0
0
votes
0
replies
1.1k
views
topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO AnnotationForge
5.2 years ago psutton • 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 65k • written 5.2 years ago by • 0
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 65k • written 5.7 years ago by • 0
1
vote
3
replies
1.1k
views
makeOrgPackageFromNCBI - cannot connect to BioMart
annotationforge
updated 5.8 years ago by 65k • written 5.8 years ago by • 0
1
vote
3
replies
1.4k
views
Running GO analysis via Prostar
prostar proteomics rforproteomics annotationforge
updated 5.9 years ago by ▴ 10 • written 5.9 years ago by ▴ 20
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
1
reply
1.3k
views
AnnotationForge, RNAseq, and non-model organism
AnnotationForge annotationforge nonmodel rnaseq
updated 6.4 years ago by 65k • written 6.4 years ago by • 0
2
votes
3
replies
1.8k
views
custom annotation for GO enrichment
annotationforge GSEA clusterprofiler GO annotation
6.7 years ago cabezasdelafuented ▴ 10
0
votes
10
replies
1.5k
views
Error during makeOrgPackageFromNCBI
annotationforge makeorgpackagefromncbi
6.8 years ago gabciamm • 0
0
votes
1
reply
1.8k
views
AnnotationForge makeOrgPackage rsqlite_send_query error
annotationforge makeorgpackage
6.9 years ago marisa.e.miller • 0
3
votes
7
replies
2.6k
views
makeOrgPackage in AnnotationForge "GID" problem
annotationforge
updated 7.1 years ago by 65k • written 7.1 years ago by • 0
0
votes
0
replies
1.2k
views
create custom 'System Biology' annotation package - class not found
AnnotationDb annotationdbi AnnotationForge
7.2 years ago Laure Cougnaud ▴ 20
3
votes
6
replies
2.6k
views
RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation microarray annotate annotationforge
7.2 years ago MOD • 0
0
votes
14
replies
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
1
vote
22
replies
4.7k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor R annotationforge
updated 7.3 years ago by ▴ 10 • written 7.8 years ago by • 0
0
votes
3
replies
1.3k
views
error while making database using Annotationforge package
annotationforge error database
updated 7.8 years ago by ★ 3.9k • written 7.8 years ago by ▴ 10
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
0
votes
1
reply
1.1k
views
errors for makeOrgPackageFromNCBI in AnnotationForge
AnnotationForge
updated 8.4 years ago by 16k • written 8.4 years ago by • 0
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
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
0
votes
5
replies
2.0k
views
Error during makeOrgPackageFromNCBI
annotation annotationforge annotationdbi makeorgpackagefromncbi
9.3 years ago oliver.tills • 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
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
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
9.6 years ago artur ▴ 80
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 9.6 years ago by ★ 7.2k • written 9.6 years ago by ▴ 80
50 results • Page 1 of 1
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Votes
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
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