Showing : annotationForge • reset
5
votes
13
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1.8k
views
Installing annotation package in locally
AnnotationDbi AnnotationHub Annotation AnnotationForge
3 months ago KABILAN • 0
2
votes
2
replies
292
views
SAS token for Annotation package
AnnotationDbi AnnotationForge
4 months ago KABILAN • 0
0
votes
3
replies
835
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
6 months ago Anna • 0
4
votes
14
replies
1.8k
views
Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() from AnnotationForge
OrganismDb AnnotationForge
8 months ago Ozan • 0
1
vote
2
replies
564
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
9 months ago Patadù ▴ 20
1
vote
8
replies
989
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 4 months ago by 68k • written 10 months ago by • 0
2
votes
28
replies
5.8k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 14 months ago by 68k • written 2.2 years ago by ▴ 10
2
votes
4
replies
1.1k
views
Question about creating custom organism database with AnnotationForge
AnnotationForge
16 months ago Adrian • 0
2
votes
5
replies
1.4k
views
Help with orgdb for non-model species via makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI
updated 16 months ago by 68k • written 16 months ago by ▴ 80
4
votes
6
replies
1.5k
views
Query regarding to create custom organism database with AnnotationForge package (AnnotationForge::makeOrgPackageFromNCBI)
AnnotationForge OrganismData OrganismDb
19 months ago abhisek001 • 0
0
votes
1
reply
2.1k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 22 months ago by 4.1k • written 22 months ago by • 0
1
vote
15
replies
3.1k
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
2.0 years ago • updated 23 months ago Mistinrain ▴ 10
0
votes
1
reply
718
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
updated 2.0 years ago by • 0 • written 2.0 years ago by ▴ 10
1
vote
1
reply
825
views
AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
AnnotationForge
2.0 years ago Mistinrain ▴ 10
0
votes
3
replies
1.1k
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
2
replies
4.7k
views
Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
biomaRt AnnotationForge
2.7 years ago Lan Anh • 0
3
votes
8
replies
3.6k
views
AnnotationForge::makeOrgPackage GO Ids mistake
AnnotationHubData AnnotationForge
2.8 years ago Saber_J ▴ 10
4
votes
2
replies
5.5k
views
Install package without updating dependent package
Install AnnotationForge
3.2 years ago 亮 • 0
0
votes
7
replies
5.9k
views
how to create an OrgDb package?
orgDb annotationForge
updated 2.8 years ago by • 0 • written 3.3 years ago by ▴ 20
1
vote
5
replies
2.0k
views
Gene ID conversion for pathway enrichment analysis of differentially expressed genes
GeneIDConversion AnnotationForge
updated 3.9 years ago by ★ 4.1k • written 3.9 years ago by • 0
0
votes
3
replies
1.6k
views
AnnotationForge: makeOrgPackageFromNCBI Error in function (type, msg, asError = TRUE) : FTP response timeout
AnnotationForge
updated 3.9 years ago by ★ 4.0k • written 4.0 years ago by • 0
2
votes
4
replies
1.3k
views
MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI NCBI SQL AnnotationForge
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
4
votes
5
replies
2.3k
views
makeOrgPackage - ERROR: Two fields in the source DB have the same name
software error AnnotationForge AnnotationDbi
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
3
votes
3
replies
1.0k
views
AnnotationForge run by three days and do not end
annotation AnnotationForge
4.8 years ago Marcelo Laia ▴ 450
1
vote
1
reply
1.9k
views
How to get GOSemSim work on custom packages built with AnnotationForge
Guangchuang Yu GOSemSim AnnotationForge
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by • 0
0
votes
4
replies
1.4k
views
AnnotationForge not working for building custom org packages
AnnotationForge Marc Carlson Hervé Pagès
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
5
votes
7
replies
2.4k
views
Problem with installing packages made by makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI gene ontology edgeR pathwayanalysis
updated 22 months ago by ▴ 50 • written 4.9 years ago by ▴ 20
0
votes
2
replies
1.5k
views
error with downloading NCBI data for makeorgpackagefromNCBI?
annotationforge makeOrgPackageFromNCBI
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
0
votes
2
replies
1.0k
views
makeOrgPackage Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name
software error go AnnotationForge AnnotationDbi
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
0
votes
0
replies
1.3k
views
topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO AnnotationForge
5.9 years ago psutton • 0
0
votes
7
replies
2.3k
views
go_bp table in custom OrgDb package
annotation go pcaExplorer AnnotationForge
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
1
vote
7
replies
1.7k
views
Error:object 'lookup_tax_id_by_organism' not found with makeOrgPackageFromNCBI
annotationforge
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
1
vote
3
replies
1.4k
views
makeOrgPackageFromNCBI - cannot connect to BioMart
annotationforge
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
1
vote
3
replies
1.6k
views
Running GO analysis via Prostar
prostar proteomics rforproteomics annotationforge
updated 6.7 years ago by ▴ 10 • written 6.7 years ago by ▴ 20
2
votes
2
replies
1.4k
views
Queries around makeOrgPackageFromNCBI
R software error annotationforge
updated 6.8 years ago by ★ 4.1k • written 6.8 years ago by • 0
0
votes
1
reply
1.6k
views
AnnotationForge, RNAseq, and non-model organism
AnnotationForge annotationforge nonmodel rnaseq
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
2
votes
3
replies
2.0k
views
custom annotation for GO enrichment
annotationforge GSEA clusterprofiler GO annotation
7.5 years ago cabezasdelafuented ▴ 10
0
votes
10
replies
1.8k
views
Error during makeOrgPackageFromNCBI
annotationforge makeorgpackagefromncbi
7.6 years ago gabciamm • 0
0
votes
1
reply
2.1k
views
AnnotationForge makeOrgPackage rsqlite_send_query error
annotationforge makeorgpackage
7.6 years ago marisa.e.miller • 0
3
votes
7
replies
3.3k
views
makeOrgPackage in AnnotationForge "GID" problem
annotationforge
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
0
votes
0
replies
1.3k
views
create custom 'System Biology' annotation package - class not found
AnnotationDb annotationdbi AnnotationForge
8.0 years ago Laure Cougnaud ▴ 20
3
votes
6
replies
3.0k
views
RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation microarray annotate annotationforge
8.0 years ago MOD • 0
0
votes
14
replies
5.6k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
8.0 years ago • updated 2.5 years ago Jenny Drnevich ★ 2.0k
1
vote
22
replies
5.4k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor R annotationforge
updated 8.1 years ago by ▴ 10 • written 8.5 years ago by • 0
0
votes
3
replies
1.6k
views
error while making database using Annotationforge package
annotationforge error database
updated 8.6 years ago by ★ 4.1k • written 8.6 years ago by ▴ 10
5
votes
22
replies
6.1k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 8.6 years ago by ★ 1.1k • written 10.0 years ago by • 0
1
vote
4
replies
3.1k
views
AnnotationForge failed due to "Parameter 0 does not have length 1"
AnnotationForge
updated 9.1 years ago by ★ 6.8k • written 9.1 years ago by • 0
0
votes
1
reply
1.3k
views
errors for makeOrgPackageFromNCBI in AnnotationForge
AnnotationForge
updated 9.2 years ago by 16k • written 9.2 years ago by • 0
0
votes
2
replies
1.8k
views
Error in makeOrgPackageFromNCBI for Medicago truncatula
annotation annotationforge
updated 9.3 years ago by 25k • written 9.3 years ago by • 0
0
votes
2
replies
1.4k
views
makeOrgPackage: possible to add option to allow GO terms now in GO.db?
annotationforge makeorgpackage go
9.7 years ago Keith Hughitt ▴ 180
50 results • Page 1 of 1
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Answer: SingleR with multiple single cell references by Aaron Lun ★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies by ATpoint ★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
Answer: To count or not to count multi-overlapping reads? by Gordon Smyth 52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2? by ATpoint ★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2? by Wolfgang Huber ★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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Popular Question to Wolfgang Huber ★ 13k
Teacher to James W. MacDonald 68k
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