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Showing :
annotationForge
•
reset
5
votes
13
replies
1.6k
views
Installing annotation package in locally
AnnotationDbi
AnnotationHub
Annotation
AnnotationForge
4 weeks ago
KABILAN
• 0
2
votes
2
replies
202
views
SAS token for Annotation package
AnnotationDbi
AnnotationForge
7 weeks ago
KABILAN
• 0
0
votes
3
replies
595
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub
AnnotationDbi
AnnotationForge
3 months ago
Anna
• 0
4
votes
14
replies
1.6k
views
Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() from AnnotationForge
OrganismDb
AnnotationForge
5 months ago
Ozan
• 0
1
vote
2
replies
423
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
6 months ago
Patadù
▴ 20
1
vote
8
replies
830
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 6 weeks ago by
James W. MacDonald
67k • written 7 months ago by
Gayatri
• 0
2
votes
28
replies
5.4k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub
AnnotationForge
Pseudomonas_aeruginosa
updated 12 months ago by
James W. MacDonald
67k • written 23 months ago by
Manmohit
▴ 10
2
votes
4
replies
994
views
Question about creating custom organism database with AnnotationForge
AnnotationForge
13 months ago
Adrian
• 0
2
votes
5
replies
1.2k
views
Help with orgdb for non-model species via makeOrgPackageFromNCBI
AnnotationForge
makeOrgPackageFromNCBI
updated 13 months ago by
James W. MacDonald
67k • written 13 months ago by
mat149
▴ 80
4
votes
6
replies
1.4k
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge
OrganismData
OrganismDb
17 months ago
abhisek001
• 0
0
votes
1
reply
1.9k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler
AnnotationForge
updated 19 months ago by
shepherl
4.1k • written 19 months ago by
yuwt8920
• 0
1
vote
15
replies
2.9k
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
22 months ago • updated 20 months ago
Mistinrain
▴ 10
0
votes
1
reply
673
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
updated 22 months ago by
jeffbrick852
• 0 • written 22 months ago by
Mistinrain
▴ 10
1
vote
1
reply
756
views
AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
AnnotationForge
22 months ago
Mistinrain
▴ 10
0
votes
3
replies
972
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb
AnnotationDbi
AnnotationForge
updated 22 months ago by
James W. MacDonald
67k • written 22 months ago by
ahiser
• 0
0
votes
2
replies
4.6k
views
Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
biomaRt
AnnotationForge
2.5 years ago
Lan Anh
• 0
3
votes
8
replies
3.3k
views
AnnotationForge::makeOrgPackage GO Ids mistake
AnnotationHubData
AnnotationForge
2.6 years ago
Saber_J
▴ 10
4
votes
2
replies
5.1k
views
Install package without updating dependent package
Install
AnnotationForge
3.0 years ago
亮
• 0
0
votes
7
replies
5.5k
views
how to create an OrgDb package?
orgDb
annotationForge
updated 2.6 years ago by
pengxinyang12
• 0 • written 3.1 years ago by
Haibo Liu
▴ 20
1
vote
5
replies
1.8k
views
Gene ID conversion for pathway enrichment analysis of differentially expressed genes
GeneIDConversion
AnnotationForge
updated 3.6 years ago by
Guido Hooiveld
★ 4.1k • written 3.7 years ago by
AbhilashKumar.Tripathi
• 0
0
votes
3
replies
1.6k
views
AnnotationForge: makeOrgPackageFromNCBI Error in function (type, msg, asError = TRUE) : FTP response timeout
AnnotationForge
updated 3.7 years ago by
Kevin Blighe
★ 4.0k • written 3.7 years ago by
Imad
• 0
2
votes
4
replies
1.2k
views
MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI
NCBI
SQL
AnnotationForge
updated 4.5 years ago by
James W. MacDonald
67k • written 4.5 years ago by
chefer
• 0
4
votes
5
replies
2.2k
views
makeOrgPackage - ERROR: Two fields in the source DB have the same name
software error
AnnotationForge
AnnotationDbi
updated 4.5 years ago by
James W. MacDonald
67k • written 4.5 years ago by
jdiaz
• 0
3
votes
3
replies
989
views
AnnotationForge run by three days and do not end
annotation
AnnotationForge
4.6 years ago
Marcelo Laia
▴ 450
1
vote
1
reply
1.6k
views
How to get GOSemSim work on custom packages built with AnnotationForge
Guangchuang Yu
GOSemSim
AnnotationForge
updated 4.6 years ago by
Kevin Blighe
★ 4.0k • written 4.6 years ago by
Cei
• 0
0
votes
4
replies
1.2k
views
AnnotationForge not working for building custom org packages
AnnotationForge
Marc Carlson
Hervé Pagès
updated 4.6 years ago by
James W. MacDonald
67k • written 4.6 years ago by
Cei
• 0
5
votes
7
replies
2.2k
views
Problem with installing packages made by makeOrgPackageFromNCBI
AnnotationForge
makeOrgPackageFromNCBI
gene ontology
edgeR
pathwayanalysis
updated 19 months ago by
L
▴ 50 • written 4.7 years ago by
babak.loghmani
▴ 20
0
votes
2
replies
1.4k
views
error with downloading NCBI data for makeorgpackagefromNCBI?
annotationforge
makeOrgPackageFromNCBI
updated 4.8 years ago by
James W. MacDonald
67k • written 4.8 years ago by
lesneski
• 0
0
votes
2
replies
966
views
makeOrgPackage Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name
software error
go
AnnotationForge
AnnotationDbi
updated 4.8 years ago by
James W. MacDonald
67k • written 4.8 years ago by
tzaquin
• 0
0
votes
0
replies
1.2k
views
topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO
AnnotationForge
5.7 years ago
psutton
• 0
0
votes
7
replies
2.2k
views
go_bp table in custom OrgDb package
annotation
go
pcaExplorer
AnnotationForge
updated 5.7 years ago by
James W. MacDonald
67k • written 5.7 years ago by
psutton
• 0
1
vote
7
replies
1.6k
views
Error:object 'lookup_tax_id_by_organism' not found with makeOrgPackageFromNCBI
annotationforge
updated 6.2 years ago by
James W. MacDonald
67k • written 6.2 years ago by
sbbinfo90
• 0
1
vote
3
replies
1.3k
views
makeOrgPackageFromNCBI - cannot connect to BioMart
annotationforge
updated 6.3 years ago by
James W. MacDonald
67k • written 6.3 years ago by
lukeholman
• 0
1
vote
3
replies
1.5k
views
Running GO analysis via Prostar
prostar
proteomics
rforproteomics
annotationforge
updated 6.5 years ago by
Samuel Wieczorek
▴ 10 • written 6.5 years ago by
lolli.langan
▴ 20
2
votes
2
replies
1.3k
views
Queries around makeOrgPackageFromNCBI
R
software error
annotationforge
updated 6.6 years ago by
Guido Hooiveld
★ 4.1k • written 6.6 years ago by
laural710
• 0
0
votes
1
reply
1.5k
views
AnnotationForge, RNAseq, and non-model organism
AnnotationForge
annotationforge
nonmodel
rnaseq
updated 6.9 years ago by
James W. MacDonald
67k • written 6.9 years ago by
mlpimsler
• 0
2
votes
3
replies
1.9k
views
custom annotation for GO enrichment
annotationforge
GSEA
clusterprofiler
GO
annotation
7.3 years ago
cabezasdelafuented
▴ 10
0
votes
10
replies
1.7k
views
Error during makeOrgPackageFromNCBI
annotationforge
makeorgpackagefromncbi
7.4 years ago
gabciamm
• 0
0
votes
1
reply
2.0k
views
AnnotationForge makeOrgPackage rsqlite_send_query error
annotationforge
makeorgpackage
7.4 years ago
marisa.e.miller
• 0
3
votes
7
replies
3.1k
views
makeOrgPackage in AnnotationForge "GID" problem
annotationforge
updated 7.6 years ago by
James W. MacDonald
67k • written 7.6 years ago by
samanthapizi
• 0
0
votes
0
replies
1.3k
views
create custom 'System Biology' annotation package - class not found
AnnotationDb
annotationdbi
AnnotationForge
7.8 years ago
Laure Cougnaud
▴ 20
3
votes
6
replies
2.9k
views
RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation
microarray
annotate
annotationforge
7.8 years ago
MOD
• 0
0
votes
14
replies
5.4k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub
AnnotationDbi
AnnotationForge
pathview
7.8 years ago • updated 2.2 years ago
Jenny Drnevich
★ 2.0k
1
vote
22
replies
5.2k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor
R
annotationforge
updated 7.9 years ago by
theobroma22
▴ 10 • written 8.3 years ago by
wssdandan2009
• 0
0
votes
3
replies
1.5k
views
error while making database using Annotationforge package
annotationforge
error
database
updated 8.3 years ago by
Guido Hooiveld
★ 4.1k • written 8.3 years ago by
kritikamish99
▴ 10
5
votes
22
replies
5.9k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor
annotationforge
annotationdbi
annotation
r
updated 8.4 years ago by
Axel Klenk
★ 1.0k • written 9.8 years ago by
Stephen H
• 0
1
vote
4
replies
3.0k
views
AnnotationForge failed due to "Parameter 0 does not have length 1"
AnnotationForge
updated 8.9 years ago by
Valerie Obenchain
★ 6.8k • written 8.9 years ago by
zhilongjia
• 0
0
votes
1
reply
1.2k
views
errors for makeOrgPackageFromNCBI in AnnotationForge
AnnotationForge
updated 9.0 years ago by
Hervé Pagès
16k • written 9.0 years ago by
songeric1107
• 0
0
votes
2
replies
1.8k
views
Error in makeOrgPackageFromNCBI for Medicago truncatula
annotation
annotationforge
updated 9.0 years ago by
Martin Morgan
25k • written 9.0 years ago by
chiapello.m
• 0
0
votes
2
replies
1.4k
views
makeOrgPackage: possible to add option to allow GO terms now in GO.db?
annotationforge
makeorgpackage
go
9.4 years ago
Keith Hughitt
▴ 180
50 results • Page
1 of 1
Recent ...
Replies
Answer: Detecting genomic signatures of drug resistance breast cancer in transcriptom
by
James W. MacDonald
67k
This support site is meant to help people with technical questions about using Bioconductor packages. Your question is probably better suit…
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
by
Paul
• 0
This is the traceback I got after running AddMotifs if this is informative? ``` 23: stop(wmsg("trying to load regions beyond the boundaries…
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
by
James W. MacDonald
67k
You will probably have to ask the Signac people. I don't know exactly what is going on under the hood for `AddMotif`, but the `EnsDb` seems…
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
by
Paul
• 0
Unfortunately I've updated my code with the newest GRCm39 genome, and yet I am still getting the same error.... Is there anything else I ca…
Comment: WGCNA with TPM tables
by
ATpoint
★ 4.5k
WGCNA is not a Bioconductor package, but generally: If you want to do serious analysis then find the raw data. There is no guarantee what …
Votes
Answer: Detecting genomic signatures of drug resistance breast cancer in transcriptom
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Comment: does anyone how to create rarefaction curves from a phyloseq object?
Answer: ANOVA like approach of edgeR
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