Showing : annotationforge • reset
5
votes
13
replies
1.6k
views
Installing annotation package in locally
AnnotationDbi AnnotationHub Annotation AnnotationForge
8 weeks ago KABILAN • 0
2
votes
2
replies
231
views
SAS token for Annotation package
AnnotationDbi AnnotationForge
11 weeks ago KABILAN • 0
0
votes
3
replies
690
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
4 months ago Anna • 0
4
votes
14
replies
1.7k
views
Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() from AnnotationForge
OrganismDb AnnotationForge
6 months ago Ozan • 0
1
vote
2
replies
476
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
7 months ago Patadù ▴ 20
1
vote
8
replies
898
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 10 weeks ago by 67k • written 8 months ago by • 0
2
votes
28
replies
5.5k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 13 months ago by 67k • written 2.0 years ago by ▴ 10
2
votes
4
replies
1.0k
views
Question about creating custom organism database with AnnotationForge
AnnotationForge
14 months ago Adrian • 0
2
votes
5
replies
1.3k
views
Help with orgdb for non-model species via makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI
updated 14 months ago by 67k • written 14 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
18 months ago abhisek001 • 0
0
votes
1
reply
2.0k
views
Error in .testForValidKeys(x, keys, keytype, fks)
clusterProfiler AnnotationForge
updated 20 months ago by 4.1k • written 20 months ago by • 0
1
vote
15
replies
2.9k
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
23 months ago • updated 21 months ago Mistinrain ▴ 10
0
votes
1
reply
693
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
updated 23 months ago by • 0 • written 23 months ago by ▴ 10
1
vote
1
reply
782
views
AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
AnnotationForge
23 months ago Mistinrain ▴ 10
0
votes
3
replies
997
views
How to handle multiple assay versions in a ChipDb annotation package
ChipDb AnnotationDbi AnnotationForge
updated 23 months ago by 67k • written 23 months ago by • 0
0
votes
2
replies
4.6k
views
Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
biomaRt AnnotationForge
2.6 years ago Lan Anh • 0
3
votes
8
replies
3.4k
views
AnnotationForge::makeOrgPackage GO Ids mistake
AnnotationHubData AnnotationForge
2.7 years ago Saber_J ▴ 10
4
votes
2
replies
5.2k
views
Install package without updating dependent package
Install AnnotationForge
3.0 years ago 亮 • 0
0
votes
7
replies
5.7k
views
how to create an OrgDb package?
orgDb annotationForge
updated 2.7 years ago by • 0 • written 3.2 years ago by ▴ 20
1
vote
5
replies
1.9k
views
Gene ID conversion for pathway enrichment analysis of differentially expressed genes
GeneIDConversion AnnotationForge
updated 3.7 years ago by ★ 4.1k • written 3.7 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 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
2
votes
4
replies
1.2k
views
MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI NCBI SQL AnnotationForge
updated 4.6 years ago by 67k • written 4.6 years ago by • 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 4.6 years ago by 67k • written 4.6 years ago by • 0
3
votes
3
replies
1.0k
views
AnnotationForge run by three days and do not end
annotation AnnotationForge
4.6 years ago Marcelo Laia ▴ 450
1
vote
1
reply
1.8k
views
How to get GOSemSim work on custom packages built with AnnotationForge
Guangchuang Yu GOSemSim AnnotationForge
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by • 0
0
votes
4
replies
1.3k
views
AnnotationForge not working for building custom org packages
AnnotationForge Marc Carlson Hervé Pagès
updated 4.7 years ago by 67k • written 4.7 years ago by • 0
5
votes
7
replies
2.3k
views
Problem with installing packages made by makeOrgPackageFromNCBI
AnnotationForge makeOrgPackageFromNCBI gene ontology edgeR pathwayanalysis
updated 20 months ago by ▴ 50 • written 4.8 years ago by ▴ 20
0
votes
2
replies
1.4k
views
error with downloading NCBI data for makeorgpackagefromNCBI?
annotationforge makeOrgPackageFromNCBI
updated 4.8 years ago by 67k • written 4.8 years ago by • 0
0
votes
2
replies
982
views
makeOrgPackage Error in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name
software error go AnnotationForge AnnotationDbi
updated 4.9 years ago by 67k • written 4.9 years ago by • 0
0
votes
0
replies
1.2k
views
topGO::annFUN.org() problem due to case-sensitivity of OrgDb field names
topGO AnnotationForge
5.8 years ago psutton • 0
0
votes
7
replies
2.2k
views
go_bp table in custom OrgDb package
annotation go pcaExplorer AnnotationForge
updated 5.8 years ago by 67k • written 5.8 years ago by • 0
1
vote
7
replies
1.7k
views
Error:object 'lookup_tax_id_by_organism' not found with makeOrgPackageFromNCBI
annotationforge
updated 6.3 years ago by 67k • written 6.3 years ago by • 0
1
vote
3
replies
1.3k
views
makeOrgPackageFromNCBI - cannot connect to BioMart
annotationforge
updated 6.4 years ago by 67k • written 6.4 years ago by • 0
1
vote
3
replies
1.6k
views
Running GO analysis via Prostar
prostar proteomics rforproteomics annotationforge
updated 6.6 years ago by ▴ 10 • written 6.6 years ago by ▴ 20
2
votes
2
replies
1.3k
views
Queries around makeOrgPackageFromNCBI
R software error annotationforge
updated 6.6 years ago by ★ 4.1k • written 6.6 years ago by • 0
0
votes
1
reply
1.6k
views
AnnotationForge, RNAseq, and non-model organism
AnnotationForge annotationforge nonmodel rnaseq
updated 7.0 years ago by 67k • written 7.0 years ago by • 0
2
votes
3
replies
2.0k
views
custom annotation for GO enrichment
annotationforge GSEA clusterprofiler GO annotation
7.4 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
7.5 years ago marisa.e.miller • 0
3
votes
7
replies
3.2k
views
makeOrgPackage in AnnotationForge "GID" problem
annotationforge
updated 7.7 years ago by 67k • written 7.7 years ago by • 0
0
votes
0
replies
1.3k
views
create custom 'System Biology' annotation package - class not found
AnnotationDb annotationdbi AnnotationForge
7.9 years ago Laure Cougnaud ▴ 20
3
votes
6
replies
2.9k
views
RSQLite::dbGetPreparedQuery() is deprecated in AnnotationForge
annotation microarray annotate annotationforge
7.9 years ago MOD • 0
0
votes
14
replies
5.5k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
7.9 years ago • updated 2.3 years ago Jenny Drnevich ★ 2.0k
1
vote
22
replies
5.3k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor R annotationforge
updated 8.0 years ago by ▴ 10 • written 8.4 years ago by • 0
0
votes
3
replies
1.6k
views
error while making database using Annotationforge package
annotationforge error database
updated 8.4 years ago by ★ 4.1k • written 8.4 years ago by ▴ 10
5
votes
22
replies
6.0k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 8.4 years ago by ★ 1.0k • written 9.8 years ago by • 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 ★ 6.8k • written 8.9 years ago by • 0
0
votes
1
reply
1.3k
views
errors for makeOrgPackageFromNCBI in AnnotationForge
AnnotationForge
updated 9.1 years ago by 16k • written 9.1 years ago by • 0
0
votes
2
replies
1.8k
views
Error in makeOrgPackageFromNCBI for Medicago truncatula
annotation annotationforge
updated 9.1 years ago by 25k • written 9.1 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
9.5 years ago Keith Hughitt ▴ 180
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
Awards • All
Popular Question to Ali Barry ▴ 40
Popular Question to gabriel.hoffman ▴ 170
Popular Question to Jenny Drnevich ★ 2.0k
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
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