Showing : annotationforge • reset
3
votes
6
replies
440
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge OrganismData OrganismDb
12 weeks ago • updated 11 weeks ago abhisek001 • 0
0
votes
1
reply
364
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 5 months ago by 3.5k • written 5 months ago by • 0
1
vote
15
replies
1.3k
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
7 months ago • updated 6 months ago Mistinrain ▴ 10
0
votes
1
reply
245
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
updated 7 months ago by • 0 • written 7 months ago by ▴ 10
1
vote
1
reply
275
views
AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
AnnotationForge
7 months ago Mistinrain ▴ 10
0
votes
3
replies
425
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 8 months ago by 63k • written 8 months ago by • 0
0
votes
11
replies
1.1k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 9 months ago by 63k • written 9 months ago by • 0
0
votes
2
replies
3.2k
views
Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
biomaRt AnnotationForge
16 months ago Lan Anh • 0
3
votes
8
replies
1.8k
views
AnnotationForge::makeOrgPackage GO Ids mistake
AnnotationHubData AnnotationForge
17 months ago Saber_J ▴ 10
3
votes
2
replies
3.2k
views
Install package without updating dependent package
Install AnnotationForge
21 months ago 亮 • 0
0
votes
7
replies
3.2k
views
how to create an OrgDb package?
orgDb annotationForge
updated 17 months ago by • 0 • written 23 months ago by • 0
1
vote
5
replies
1.1k
views
Gene ID conversion for pathway enrichment analysis of differentially expressed genes
GeneIDConversion AnnotationForge
updated 2.5 years ago by ★ 3.7k • written 2.5 years ago by • 0
0
votes
3
replies
1.1k
views
AnnotationForge: makeOrgPackageFromNCBI Error in function (type, msg, asError = TRUE) : FTP response timeout
AnnotationForge
updated 2.5 years ago by 3.8k • written 2.5 years ago by • 0
2
votes
4
replies
755
views
MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI NCBI SQL AnnotationForge
updated 3.4 years ago by 63k • written 3.4 years ago by • 0
4
votes
5
replies
1.5k
views
makeOrgPackage - ERROR: Two fields in the source DB have the same name
software error AnnotationForge AnnotationDbi
updated 3.4 years ago by 63k • written 3.4 years ago by • 0
3
votes
3
replies
527
views
AnnotationForge run by three days and do not end
annotation AnnotationForge
3.4 years ago Marcelo Laia ▴ 450
1
vote
1
reply
1.0k
views
How to get GOSemSim work on custom packages built with AnnotationForge
Guangchuang Yu GOSemSim AnnotationForge
updated 3.4 years ago by 3.8k • written 3.4 years ago by • 0
0
votes
4
replies
671
views
AnnotationForge not working for building custom org packages
AnnotationForge Marc Carlson Hervé Pagès
updated 3.4 years ago by 63k • written 3.4 years ago by • 0
5
votes
7
replies
1.2k
views
Problem with installing packages made by makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI gene ontology edgeR pathwayanalysis
updated 5 months ago by ▴ 50 • written 3.5 years ago by ▴ 20
0
votes
2
replies
808
views
error with downloading NCBI data for makeorgpackagefromNCBI?
annotationforge makeOrgPackageFromNCBI
updated 3.6 years ago by 63k • written 3.6 years ago by • 0
0
votes
2
replies
598
views
makeOrgPackage Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name
software error go AnnotationForge AnnotationDbi
updated 3.7 years ago by 63k • written 3.7 years ago by • 0
0
votes
0
replies
886
views
topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO AnnotationForge
4.5 years ago psutton • 0
0
votes
7
replies
1.4k
views
go_bp table in custom OrgDb package
annotation go pcaExplorer AnnotationForge
updated 4.5 years ago by 63k • written 4.5 years ago by • 0
1
vote
7
replies
1.1k
views
Error:object 'lookup_tax_id_by_organism' not found with makeOrgPackageFromNCBI
annotationforge
updated 5.1 years ago by 63k • written 5.1 years ago by • 0
1
vote
3
replies
886
views
makeOrgPackageFromNCBI - cannot connect to BioMart
annotationforge
updated 5.1 years ago by 63k • written 5.1 years ago by • 0
1
vote
3
replies
1.1k
views
Running GO analysis via Prostar
prostar proteomics rforproteomics annotationforge
updated 5.3 years ago by ▴ 10 • written 5.3 years ago by ▴ 20
2
votes
2
replies
855
views
Queries around makeOrgPackageFromNCBI
R software error annotationforge
updated 5.4 years ago by ★ 3.7k • written 5.4 years ago by • 0
0
votes
1
reply
1.1k
views
AnnotationForge, RNAseq, and non-model organism
AnnotationForge annotationforge nonmodel rnaseq
updated 5.8 years ago by 63k • written 5.8 years ago by • 0
2
votes
3
replies
1.5k
views
custom annotation for GO enrichment
annotationforge GSEA clusterprofiler GO annotation
6.1 years ago cabezasdelafuented ▴ 10
0
votes
10
replies
1.2k
views
Error during makeOrgPackageFromNCBI
annotationforge makeorgpackagefromncbi
6.2 years ago gabciamm • 0
0
votes
1
reply
1.6k
views
AnnotationForge makeOrgPackage rsqlite_send_query error
annotationforge makeorgpackage
6.2 years ago marisa.e.miller • 0
3
votes
7
replies
2.1k
views
makeOrgPackage in AnnotationForge "GID" problem
annotationforge
updated 6.4 years ago by 63k • written 6.4 years ago by • 0
0
votes
0
replies
970
views
create custom 'System Biology' annotation package - class not found
AnnotationDb annotationdbi AnnotationForge
6.6 years ago Laure Cougnaud ▴ 20
3
votes
6
replies
2.3k
views
RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation microarray annotate annotationforge
6.6 years ago MOD • 0
0
votes
14
replies
4.1k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
6.6 years ago • updated 13 months ago Jenny Drnevich ★ 2.0k
1
vote
22
replies
3.9k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor R annotationforge
updated 6.7 years ago by ▴ 10 • written 7.1 years ago by • 0
0
votes
3
replies
1.1k
views
error while making database using Annotationforge package
annotationforge error database
updated 7.2 years ago by ★ 3.7k • written 7.2 years ago by ▴ 10
5
votes
22
replies
5.0k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 7.2 years ago by ▴ 990 • written 8.6 years ago by • 0
1
vote
4
replies
2.4k
views
AnnotationForge failed due to "Parameter 0 does not have length 1"
AnnotationForge
updated 7.7 years ago by ★ 6.8k • written 7.7 years ago by • 0
0
votes
1
reply
924
views
errors for makeOrgPackageFromNCBI in AnnotationForge
AnnotationForge
updated 7.8 years ago by 16k • written 7.8 years ago by • 0
0
votes
2
replies
1.4k
views
Error in makeOrgPackageFromNCBI for Medicago truncatula
annotation annotationforge
updated 7.9 years ago by 25k • written 7.9 years ago by • 0
0
votes
2
replies
1.1k
views
makeOrgPackage: possible to add option to allow GO terms now in GO.db?
annotationforge makeorgpackage go
8.3 years ago Keith Hughitt ▴ 180
0
votes
5
replies
1.8k
views
Error during makeOrgPackageFromNCBI
annotation annotationforge annotationdbi makeorgpackagefromncbi
8.7 years ago • updated 8.6 years ago oliver.tills • 0
0
votes
4
replies
2.0k
views
IlluminaHumanMethylation450k.db has undeclared dependency on AnnotationForge
annotationforge
updated 9.0 years ago by ★ 7.2k • written 9.0 years ago by ★ 3.7k
1
vote
2
replies
1.8k
views
AnnotationForge: org.Xx.eg.db created with makeOrgPackage() is missing org.Xx.egGO object.
organismdb annotationdbi annotationforge
updated 9.0 years ago by ★ 7.2k • written 9.0 years ago by ▴ 80
3
votes
9
replies
2.5k
views
Create object "Go3AnnDbBimap" and include it in a org.Xx.eg.db package to use with goProfiles and goTools
goprofiles AnnotationForge Bimap GO
9.0 years ago artur ▴ 80
3
votes
3
replies
8.3k
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 9.0 years ago by ★ 7.2k • written 9.0 years ago by ▴ 80
0
votes
0
replies
1.0k
views
Failure to Install Organism Package from AnnotationForge
Organism AnnotationDbi AnnotationForge Organism AnnotationDbi AnnotationForge
9.6 years ago Guest User ★ 12k
1
vote
1
reply
1.7k
views
Mapping Affymetrix annotations with Bioconductor annotations
Annotation Organism zebrafish cdf affy AnnotationForge Annotation Organism zebrafish cdf
updated 10.0 years ago by 63k • written 10.0 years ago by ▴ 80
0
votes
1
reply
1.3k
views
Error using makeDBPackage() from AnnotationForge package
Annotation probe AnnotationForge Annotation probe AnnotationForge
updated 10.0 years ago by ★ 7.2k • written 10.0 years ago by ▴ 80
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Answer: ukb Chromosomal position information was converted into SNPS by James W. MacDonald 63k
In my work, we almost always convert RSIDs to chr:pos because the former is ambiguous and changing whereas the latter is not. Which is like…
Comment: T.fit function of maSigPro returns error message by hanna.g • 0
Addition to the issue above: the T.fit function works only when choosing the step.method = "forward", for whatever reason. Maybe this clue …
Answer: Deseq2, enrichGO and ensembl ID by James W. MacDonald 63k
1. There isn't a keytype alternative. You need the gene IDs. 2. Convert the `rownames` of your 'se' object, or the `rownames` of your `D…
Comment: Doubts regarding Pathview by loyedbend2811 • 0
I thoroughly enjoyed reading your essay, and it was quite beneficial to me. Please join me in [monopoly online][1] if you have the time. …
Comment: ukb Chromosomal position information was converted into SNPS by wenbo • 0
Hi, I downloaded uk biobank data, but I don't know how to use R to convert chromosome position information to rs
Votes
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
Comment: comparing contrasts in edger/lima using makeContrasts function
Answer: comparing contrasts in edger/lima using makeContrasts function
Answer: Differential expression analysis with only FPKM matrix available from total newb
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