Showing : Annotationhub • reset
10
votes
44
replies
11k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 13 days ago by • 0 • written 7.2 years ago by ★ 4.1k
7
votes
44
replies
8.5k
views
OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 6.5 years ago by 4.3k • written 6.6 years ago by ▴ 10
2
votes
28
replies
7.4k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 2.2 years ago by 68k • written 3.1 years ago by ▴ 10
9
votes
21
replies
17k
views
ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tb…
AnnotationHub dplyr
updated 3.5 years ago by ▴ 10 • written 5.2 years ago by ▴ 40
4
votes
17
replies
3.9k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by ▴ 10
8
votes
16
replies
9.8k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 5.5 years ago by 4.3k • written 5.5 years ago by ▴ 680
0
votes
14
replies
6.4k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
9.0 years ago • updated 3.4 years ago Jenny Drnevich ★ 2.0k
9
votes
14
replies
10k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 18 months ago by 4.3k • written 4.0 years ago by ▴ 40
3
votes
13
replies
3.9k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub organismdb orgdb unsupported organisms
updated 10.0 years ago by ★ 6.8k • written 10.0 years ago by ★ 4.1k
5
votes
13
replies
2.5k
views
Installing annotation package in locally
AnnotationDbi AnnotationHub Annotation AnnotationForge
15 months ago KABILAN • 0
11
votes
13
replies
6.9k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
5.2 years ago • updated 5.0 years ago rohitsatyam102 ▴ 20
2
votes
12
replies
3.4k
views
AnnotationHub-cant extract database
annotationhub
updated 8.8 years ago by ★ 6.8k • written 8.8 years ago by • 0
2
votes
12
replies
4.4k
views
Error: failed to load 'AnnotationHub' resource
biomart annotationhub
updated 10.2 years ago by 25k • written 10.2 years ago by ▴ 10
6
votes
12
replies
8.8k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
2.2 years ago • updated 21 months ago shepherl 4.3k
5
votes
11
replies
4.1k
views
Certificate problem with ExperimentHub / AnnotationHub
software error curatedmetagenomicdata annotationhub experimenthub
updated 9.1 years ago by ★ 1.1k • written 9.1 years ago by ▴ 10
3
votes
11
replies
8.1k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 23 months ago by ★ 4.1k • written 5.0 years ago by • 0
0
votes
11
replies
2.9k
views
AH134 and other AnnotationHub objects unavailable as "defunct"
AnnotationHub
updated 6.7 years ago by 4.3k • written 6.7 years ago by ▴ 40
7
votes
11
replies
7.1k
views
Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.probes
edgeR limma annotationhub kegga annotationdbi
updated 9.6 years ago by ▴ 20 • written 9.9 years ago by ▴ 20
2
votes
10
replies
3.7k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 4.3 years ago by ★ 4.1k • written 4.3 years ago by • 0
4
votes
10
replies
1.8k
views
Suggestion: spinning wheel for AnnotationHub
annotationhub
updated 8.3 years ago by 4.3k • written 8.4 years ago by 43k
3
votes
9
replies
4.9k
views
AnnotationHub corrupt database
annotationhub
updated 6.9 years ago by 4.3k • written 10.5 years ago by ▴ 180
4
votes
8
replies
3.2k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
4.1 years ago • updated 3.7 years ago nattzy94 ▴ 20
0
votes
8
replies
3.2k
views
Usecase_AnnotationHub_GRanges.Rmd, genes = qhs[[1]] can't download UCSC 'refGene'. - Window 7, R 3.2.1, RStudio 0.99.484
annotationhub bioconductor for genomic data science
10.4 years ago J.C. SUN • 0
2
votes
8
replies
2.3k
views
Problem fetching resources from AnnotationHub, error 403
AnnotationHub
updated 10.2 years ago by ★ 6.8k • written 10.2 years ago by ★ 2.1k
0
votes
8
replies
4.0k
views
I can't use AnnotationHub()
AnnotationHub
6.0 years ago 755606975 • 0
2
votes
8
replies
3.0k
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error enrichGO annotationHub clusterProfiler Job
updated 5.7 years ago by 68k • written 5.7 years ago by • 0
1
vote
7
replies
2.0k
views
mismatch between AnnotationHub ensembl v71 hsapiens and direct download using rtracklayer
annotationhub
updated 9.0 years ago by ★ 6.8k • written 9.0 years ago by ▴ 10
1
vote
7
replies
1.5k
views
News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
7.3 years ago shepherl 4.3k
4
votes
7
replies
2.4k
views
AnnotationHub and ExperimentHub make "~" directory in my home
annotationhub experimenthub
updated 9.4 years ago by ★ 6.8k • written 9.4 years ago by 43k
3
votes
6
replies
3.6k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 3.5 years ago by 4.3k • written 5.7 years ago by ★ 2.0k
4
votes
6
replies
4.3k
views
OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)
AnnotationHub OrganismDbi org.Hs.eg.db
updated 3.9 years ago by 53k • written 3.9 years ago by • 0
2
votes
6
replies
2.1k
views
R getting "stuck" with RoadMap resource retrieval through AnnotationHub
roadmap project annotationhub
8.7 years ago vanesa_1230 • 0
1
vote
6
replies
3.1k
views
Problem with AnnotationHub()
annotationhub
updated 9.1 years ago by ★ 6.8k • written 9.1 years ago by ▴ 10
1
vote
6
replies
4.6k
views
failed to load 'AnnotationHub' resource
annotationhub annotation error
10.1 years ago elhananby ▴ 10
0
votes
6
replies
1.8k
views
initialization of AnnotationHub() in version 2.12.0 is problematically verbose
AnnotationHub
updated 7.7 years ago by 25k • written 7.7 years ago by ▴ 40
1
vote
6
replies
1.8k
views
unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 21 months ago by ▴ 230 • written 21 months ago by • 0
0
votes
6
replies
2.2k
views
Why are important organisms missing from AnnotationHub. Example query(hub, "Zea")
orgdb annotationhub
8.5 years ago slbai01 • 0
0
votes
5
replies
1.9k
views
AnnotationHub() returns only one record !?
annotationhub
updated 9.9 years ago by ★ 6.8k • written 9.9 years ago by • 0
0
votes
5
replies
1.9k
views
annotationhub: data update
annotationhub
updated 7.4 years ago by 4.3k • written 7.4 years ago by ★ 6.5k
1
vote
5
replies
2.3k
views
EnsDb: bad_weak_ptr
AnnotationHub BiocFileCache
19 months ago Lluís Revilla Sancho ▴ 760
0
votes
5
replies
2.3k
views
Cannot connect to annotationhub server
AnnotationHub ExperimentHub
updated 19 months ago by 4.3k • written 19 months ago by • 0
0
votes
5
replies
2.6k
views
Why are important organisms missing from AnnotationHub() $rdataclass == "OrgDb"?
annotationhub orgdb
updated 10.2 years ago by ★ 6.8k • written 10.2 years ago by ▴ 10
1
vote
5
replies
2.5k
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 5.8 years ago by 4.3k • written 5.8 years ago by • 0
0
votes
4
replies
2.0k
views
AnnotationHub
AnnotationHub
3.8 years ago junliqilinpan • 0
0
votes
4
replies
2.8k
views
AnnotationHub Error HTTP status was '500 Internal Server Error'
annotationhub software error
10.0 years ago ness • 0
5
votes
4
replies
2.1k
views
Eliminating repetitive calls to ExperimentHub
experimenthub annotationhub large dataset
7.7 years ago slinker ▴ 20
1
vote
4
replies
1.7k
views
Create a GmapGenome from a FaFile from AnnotationHub
gmapr gmapgenome annotationhub fafile
updated 10.2 years ago by ★ 11k • written 10.2 years ago by ★ 2.1k
0
votes
4
replies
1.6k
views
error with downloading AnnotationHub item AH134
AnnotationHub
updated 9.3 years ago by ★ 6.8k • written 9.3 years ago by ▴ 40
1
vote
4
replies
1.8k
views
AnnotationHub Server denied you to change the given directory
annotation annotationhub
updated 6.7 years ago by 4.3k • written 6.7 years ago by ▴ 10
0
votes
4
replies
2.0k
views
Error in GOFrame due to NA for unsupported organism (Gene Ontology)
reportingtools annotationhub gostats
updated 9.5 years ago by 68k • written 9.5 years ago by ▴ 20
131 results • Page 1 of 3
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Replies
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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