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Showing :
annotationForge
•
reset
3
votes
6
replies
441
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge
OrganismData
OrganismDb
12 weeks ago
abhisek001
• 0
0
votes
1
reply
365
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler
AnnotationForge
updated 5 months ago by
shepherl
3.5k • written 5 months ago by
yuwt8920
• 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
246
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
updated 7 months ago by
jeffbrick852
• 0 • written 7 months ago by
Mistinrain
▴ 10
1
vote
1
reply
277
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
James W. MacDonald
63k • written 8 months ago by
ahiser
• 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
James W. MacDonald
63k • written 9 months ago by
Manmohit
• 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
pengxinyang12
• 0 • written 23 months ago by
Haibo Liu
• 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
Guido Hooiveld
★ 3.7k • written 2.5 years ago by
AbhilashKumar.Tripathi
• 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
Kevin Blighe
3.8k • written 2.5 years ago by
Imad
• 0
2
votes
4
replies
757
views
MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI
NCBI
SQL
AnnotationForge
updated 3.4 years ago by
James W. MacDonald
63k • written 3.4 years ago by
chefer
• 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
James W. MacDonald
63k • written 3.4 years ago by
jdiaz
• 0
3
votes
3
replies
529
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
Kevin Blighe
3.8k • written 3.4 years ago by
Cei
• 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
James W. MacDonald
63k • written 3.4 years ago by
Cei
• 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
L
▴ 50 • written 3.5 years ago by
babak.loghmani
▴ 20
0
votes
2
replies
808
views
error with downloading NCBI data for makeorgpackagefromNCBI?
annotationforge
makeOrgPackageFromNCBI
updated 3.6 years ago by
James W. MacDonald
63k • written 3.6 years ago by
lesneski
• 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
James W. MacDonald
63k • written 3.7 years ago by
tzaquin
• 0
0
votes
0
replies
887
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 4.6 years ago by
James W. MacDonald
63k • written 4.6 years ago by
psutton
• 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
James W. MacDonald
63k • written 5.1 years ago by
sbbinfo90
• 0
1
vote
3
replies
887
views
makeOrgPackageFromNCBI - cannot connect to BioMart
annotationforge
updated 5.2 years ago by
James W. MacDonald
63k • written 5.2 years ago by
lukeholman
• 0
1
vote
3
replies
1.1k
views
Running GO analysis via Prostar
prostar
proteomics
rforproteomics
annotationforge
updated 5.3 years ago by
Samuel Wieczorek
▴ 10 • written 5.3 years ago by
lolli.langan
▴ 20
2
votes
2
replies
857
views
Queries around makeOrgPackageFromNCBI
R
software error
annotationforge
updated 5.4 years ago by
Guido Hooiveld
★ 3.7k • written 5.4 years ago by
laural710
• 0
0
votes
1
reply
1.1k
views
AnnotationForge, RNAseq, and non-model organism
AnnotationForge
annotationforge
nonmodel
rnaseq
updated 5.8 years ago by
James W. MacDonald
63k • written 5.8 years ago by
mlpimsler
• 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
James W. MacDonald
63k • written 6.4 years ago by
samanthapizi
• 0
0
votes
0
replies
971
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
theobroma22
▴ 10 • written 7.1 years ago by
wssdandan2009
• 0
0
votes
3
replies
1.1k
views
error while making database using Annotationforge package
annotationforge
error
database
updated 7.2 years ago by
Guido Hooiveld
★ 3.7k • written 7.2 years ago by
kritikamish99
▴ 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
Axel Klenk
▴ 990 • written 8.6 years ago by
Stephen H
• 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
Valerie Obenchain
★ 6.8k • written 7.7 years ago by
zhilongjia
• 0
0
votes
1
reply
924
views
errors for makeOrgPackageFromNCBI in AnnotationForge
AnnotationForge
updated 7.8 years ago by
Hervé Pagès
16k • written 7.8 years ago by
songeric1107
• 0
0
votes
2
replies
1.4k
views
Error in makeOrgPackageFromNCBI for Medicago truncatula
annotation
annotationforge
updated 7.9 years ago by
Martin Morgan
25k • written 7.9 years ago by
chiapello.m
• 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
Marc Carlson
★ 7.2k • written 9.0 years ago by
Simon Anders
★ 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
Marc Carlson
★ 7.2k • written 9.0 years ago by
artur
▴ 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
Marc Carlson
★ 7.2k • written 9.0 years ago by
artur
▴ 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
James W. MacDonald
63k • written 10.0 years ago by
Joao Sollari Lopes
▴ 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
Marc Carlson
★ 7.2k • written 10.0 years ago by
gabriel teku
▴ 80
50 results • Page
1 of 1
Recent ...
Replies
Comment: DMRcate design
by
Jitendra
▴ 10
Thanks James, do I also need to mention 'contrasts=FALSE' in cpg.annotate. Thanks a lot for your all help and time.
Comment: Speeding up of DelayedArray::write_block()
by
Koki
▴ 10
I don't know the details but do you mean using `HDF5RealizationSink` or `TENxRealizationSink` will make it possible to writing sparse multi…
Comment: DelayedArray::read_sparse_block
by
Koki
▴ 10
Ok, I understood. How about "writing" to HDF5? Are you going to implement `write_block_as_sparse` in `SparseArray` package?
Comment: DelayedArray::read_sparse_block
by
Hervé Pagès
16k
> So do you means the specification change from DelayedArray's read_sparse_block to SparseArray's read_block_as_sparse will accelerate the …
Comment: DelayedArray::read_sparse_block
by
Koki
▴ 10
Thanks for your reply. So do you means the specification change from `DelayedArray`'s `read_sparse_block` to `SparseArray`'s `read_block_a…
Votes
Answer: DMRcate design
Answer: DMRcate design
Comment: DMRcate design
Answer: What MetaPhlAn3 database was used in cMD 3?
Comment: Speeding up of DelayedArray::write_block()
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