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AnnotationForge
•
reset
0
votes
4
replies
159
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
2 days ago • updated 2 hours ago
Gayatri
• 0
2
votes
28
replies
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
James W. MacDonald
65k • written 16 months ago by
Manmohit
▴ 10
2
votes
4
replies
674
views
Question about creating custom organism database with AnnotationForge
AnnotationForge
6 months ago
Adrian
• 0
2
votes
5
replies
747
views
Help with orgdb for non-model species via makeOrgPackageFromNCBI
AnnotationForge
makeOrgPackageFromNCBI
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
mat149
▴ 70
3
votes
6
replies
941
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge
OrganismData
OrganismDb
10 months ago • updated 9 months ago
abhisek001
• 0
0
votes
1
reply
1.0k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler
AnnotationForge
updated 12 months ago by
shepherl
3.8k • written 12 months ago by
yuwt8920
• 0
1
vote
15
replies
2.2k
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
14 months ago • updated 13 months ago
Mistinrain
▴ 10
0
votes
1
reply
472
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
updated 14 months ago by
jeffbrick852
• 0 • written 14 months ago by
Mistinrain
▴ 10
1
vote
1
reply
510
views
AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
AnnotationForge
15 months ago
Mistinrain
▴ 10
0
votes
3
replies
734
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb
AnnotationDbi
AnnotationForge
updated 15 months ago by
James W. MacDonald
65k • written 15 months ago by
ahiser
• 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
3
votes
8
replies
2.5k
views
AnnotationForge::makeOrgPackage GO Ids mistake
AnnotationHubData
AnnotationForge
2.0 years ago • updated 24 months ago
Saber_J
▴ 10
4
votes
2
replies
4.0k
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 2.0 years ago by
pengxinyang12
• 0 • written 2.5 years ago by
Haibo Liu
• 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
Guido Hooiveld
★ 3.9k • written 3.1 years ago by
AbhilashKumar.Tripathi
• 0
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
Kevin Blighe
★ 3.9k • written 3.1 years ago by
Imad
• 0
2
votes
4
replies
988
views
MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI
NCBI
SQL
AnnotationForge
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
chefer
• 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
James W. MacDonald
65k • written 4.0 years ago by
jdiaz
• 0
3
votes
3
replies
750
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
Kevin Blighe
★ 3.9k • written 4.0 years ago by
Cei
• 0
0
votes
4
replies
927
views
AnnotationForge not working for building custom org packages
AnnotationForge
Marc Carlson
Hervé Pagès
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
Cei
• 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
L
▴ 50 • written 4.1 years ago by
babak.loghmani
▴ 20
0
votes
2
replies
1.1k
views
error with downloading NCBI data for makeorgpackagefromNCBI?
annotationforge
makeOrgPackageFromNCBI
updated 4.2 years ago by
James W. MacDonald
65k • written 4.2 years ago by
lesneski
• 0
0
votes
2
replies
793
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
James W. MacDonald
65k • written 4.2 years ago by
tzaquin
• 0
0
votes
0
replies
1.1k
views
topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO
AnnotationForge
5.1 years ago
psutton
• 0
0
votes
7
replies
1.8k
views
go_bp table in custom OrgDb package
annotation
go
pcaExplorer
AnnotationForge
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
psutton
• 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
James W. MacDonald
65k • written 5.7 years ago by
sbbinfo90
• 0
1
vote
3
replies
1.1k
views
makeOrgPackageFromNCBI - cannot connect to BioMart
annotationforge
updated 5.7 years ago by
James W. MacDonald
65k • written 5.7 years ago by
lukeholman
• 0
1
vote
3
replies
1.3k
views
Running GO analysis via Prostar
prostar
proteomics
rforproteomics
annotationforge
updated 5.9 years ago by
Samuel Wieczorek
▴ 10 • written 5.9 years ago by
lolli.langan
▴ 20
2
votes
2
replies
1.1k
views
Queries around makeOrgPackageFromNCBI
R
software error
annotationforge
updated 6.0 years ago by
Guido Hooiveld
★ 3.9k • written 6.0 years ago by
laural710
• 0
0
votes
1
reply
1.3k
views
AnnotationForge, RNAseq, and non-model organism
AnnotationForge
annotationforge
nonmodel
rnaseq
updated 6.4 years ago by
James W. MacDonald
65k • written 6.4 years ago by
mlpimsler
• 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
1.4k
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
6.8 years ago
marisa.e.miller
• 0
3
votes
7
replies
2.6k
views
makeOrgPackage in AnnotationForge "GID" problem
annotationforge
updated 7.0 years ago by
James W. MacDonald
65k • written 7.0 years ago by
samanthapizi
• 0
0
votes
0
replies
1.1k
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
4.6k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor
R
annotationforge
updated 7.3 years ago by
theobroma22
▴ 10 • written 7.7 years ago by
wssdandan2009
• 0
0
votes
3
replies
1.3k
views
error while making database using Annotationforge package
annotationforge
error
database
updated 7.8 years ago by
Guido Hooiveld
★ 3.9k • written 7.8 years ago by
kritikamish99
▴ 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
Axel Klenk
★ 1.0k • written 9.2 years ago by
Stephen H
• 0
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
Valerie Obenchain
★ 6.8k • written 8.3 years ago by
zhilongjia
• 0
0
votes
1
reply
1.1k
views
errors for makeOrgPackageFromNCBI in AnnotationForge
AnnotationForge
updated 8.4 years ago by
Hervé Pagès
16k • written 8.4 years ago by
songeric1107
• 0
0
votes
2
replies
1.6k
views
Error in makeOrgPackageFromNCBI for Medicago truncatula
annotation
annotationforge
updated 8.5 years ago by
Martin Morgan
25k • written 8.5 years ago by
chiapello.m
• 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
0
votes
5
replies
2.0k
views
Error during makeOrgPackageFromNCBI
annotation
annotationforge
annotationdbi
makeorgpackagefromncbi
9.3 years ago • updated 9.2 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
Marc Carlson
★ 7.2k • written 9.6 years ago by
Simon Anders
★ 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
Marc Carlson
★ 7.2k • written 9.6 years ago by
artur
▴ 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
8.6k
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
Marc Carlson
★ 7.2k • written 9.6 years ago by
artur
▴ 80
50 results • Page
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Replies
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
Guangchuang Yu
★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO
by
Guido Hooiveld
★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference
by
ATpoint
★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Votes
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
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