Showing : AnnotationHub • reset
1
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127
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Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb Bioconductor AnnotationHub clusterProfiler
updated 5 weeks ago by ★ 3.0k • written 5 weeks ago by • 0
0
votes
1
reply
110
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News: Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache AnnotationHub ExperimentHub cache
10 weeks ago shepherl 2.7k
0
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2
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220
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Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub biomaRt
12 weeks ago rohitsatyam102 ▴ 10
1
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2
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239
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GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 4 months ago by ★ 3.0k • written 4 months ago by • 0
11
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13
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650
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How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
6 months ago • updated 4 months ago rohitsatyam102 ▴ 10
5
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20
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6.1k
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ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tb…
AnnotationHub dplyr
7 months ago • updated 4 months ago georgia.katsoula ▴ 10
3
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2
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402
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Issue with AnnotationHub
AnnotationHub
6 months ago rahnaman ▴ 10
1
vote
2
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180
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How to mimic biomaRt results with AnnotationHub?
biomaRt AnnotationHub
7 months ago Ezgi ▴ 30
1
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3
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162
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AnnotationHub: failed to load resource name
AnnotationHub
9 months ago ben.ponv • 0
4
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17
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521
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 9 months ago by 3.1k • written 9 months ago by ▴ 10
4
votes
2
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223
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News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
9 months ago Johannes Rainer ★ 1.9k
7
votes
16
replies
686
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 10 months ago by 2.7k • written 10 months ago by ▴ 570
0
votes
2
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168
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Can't select GO from AnnotationHub orgDB packages
GO.db AnnotationHub OrgDB
updated 11 months ago by 57k • written 11 months ago by ★ 2.0k
0
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3
replies
176
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 12 months ago by 57k • written 12 months ago by ▴ 610
1
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4
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164
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How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 13 months ago by 2.7k • written 13 months ago by ★ 2.0k
2
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8
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246
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gene enrichment using enrichGO function throuth annotationHub orgDb
software error enrichGO annotationHub clusterProfiler Job
updated 13 months ago by 57k • written 13 months ago by • 0
1
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5
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190
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 14 months ago by 2.7k • written 14 months ago by • 0
0
votes
2
replies
100
views
hg38 tracks for AnnotationHub
annotationhub
15 months ago Michael Love 33k
0
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1
reply
118
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AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 15 months ago by 2.7k • written 15 months ago by • 0
0
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8
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457
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I can't use AnnotationHub()
AnnotationHub
17 months ago 755606975 • 0
1
vote
3
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709
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AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub Ensembl Mouse AnnotationHub Ensembl
18 months ago dmgatti ▴ 10
3
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0
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231
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News: EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation ensembldb EnsDb AnnotationHub News
18 months ago Johannes Rainer ★ 1.9k
0
votes
2
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248
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how to choose annotation file in AnnotationHub web server
annotation AnnotationHub
19 months ago 15958021290 ▴ 10
3
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4
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253
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Are AH52264, AH66175, and AH70594 duplicates?
AnnotationHub
updated 20 months ago by 2.7k • written 20 months ago by ▴ 120
1
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3
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213
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Problem with AnnotationHub after crash during first download of metadata
AnnotationHub
updated 21 months ago by 2.7k • written 22 months ago by ▴ 10
7
votes
44
replies
1.1k
views
OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 23 months ago by 2.7k • written 2.0 years ago by • 0
2
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0
replies
265
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News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 2.1 years ago by • 0 • written 2.1 years ago by 2.7k
1
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4
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239
views
AnnotationHub Server denied you to change the given directory
annotation annotationhub
updated 2.1 years ago by 2.7k • written 2.1 years ago by ▴ 10
0
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11
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471
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AH134 and other AnnotationHub objects unavailable as "defunct"
AnnotationHub
updated 2.1 years ago by 2.7k • written 2.1 years ago by ▴ 40
1
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1
reply
279
views
The total genes items (e.g. ENTREZ ID, SYMBOL) in OrgDb (Salmo salar; [["AH66207"]]) is just half the gene number in NCBI ?!
Annotationhub Annotationdb profiler annotationdbi
2.2 years ago wecai • 0
3
votes
9
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2.4k
views
AnnotationHub corrupt database
annotationhub
updated 2.3 years ago by 2.7k • written 5.9 years ago by ▴ 180
0
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0
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309
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News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
2.3 years ago shepherl 2.7k
5
votes
10
replies
846
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 5 months ago by ★ 1.9k • written 2.6 years ago by ★ 3.0k
1
vote
7
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435
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News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
2.7 years ago shepherl 2.7k
0
votes
5
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442
views
annotationhub: data update
annotationhub
updated 2.8 years ago by 2.7k • written 2.8 years ago by 6.5k
0
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0
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386
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News: ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit annotationdata News
2.9 years ago shepherl 2.7k
1
vote
2
replies
556
views
AnnotationHub, force update snapshot date?
annotationhub
updated 2.9 years ago by 2.7k • written 2.9 years ago by ▴ 70
5
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4
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594
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Eliminating repetitive calls to ExperimentHub
experimenthub annotationhub large dataset
3.1 years ago slinker ▴ 20
0
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6
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616
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initialization of AnnotationHub() in version 2.12.0 is problematically verbose
AnnotationHub
updated 3.1 years ago by 25k • written 3.1 years ago by ▴ 40
0
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0
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477
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News: ensembl 92 gtfs and fasta twobits have been added to AnnotationHub
ensembl gtf 2bit annotationhub News
3.2 years ago shepherl 2.7k
1
vote
0
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766
views
News: ensembl 91 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit News
3.5 years ago shepherl 2.7k
0
votes
1
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604
views
News: OrgDbs in AnnotationHub
annotationhub orgdb News
3.6 years ago shepherl 2.7k
0
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0
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555
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News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
3.6 years ago shepherl 2.7k
0
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2
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504
views
Trouble loading Roadmap data from AnnotationHub
annotationhub
updated 3.7 years ago by 2.7k • written 3.7 years ago by • 0
1
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0
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703
views
Error: failed to load resource reason: invalid class GRanges object: seqnames(x) contains missing values for newer GRCh38 annotations
AnnotationHub
3.7 years ago marcel.schilling ▴ 10
0
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2
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510
views
AnnotationHub downloading dataset fail
annotationhub download_error
updated 3.7 years ago by 57k • written 3.7 years ago by • 0
4
votes
10
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674
views
Suggestion: spinning wheel for AnnotationHub
annotationhub
updated 3.7 years ago by 2.7k • written 3.8 years ago by 33k
0
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1
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648
views
querying annotation hub for common TF, in common cell line returns no results....
annotate annotationhub
updated 3.8 years ago by 2.7k • written 3.8 years ago by ▴ 50
1
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0
replies
814
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News: ensembl 90 ensembldb EnsDb databases have been added to AnnotationHub
ensemblb ensembl AnnotationHub annotation News
3.8 years ago Johannes Rainer ★ 1.9k
1
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0
replies
636
views
News: ensembl 90 gtfs and fasta twobits have been added to AnnotationHub
annotationhub bioconductor News
updated 3.8 years ago by 25k • written 3.8 years ago by 2.7k
50 results • Page 1 of 1
Recent ...
Replies
Comment: Data input for aracne2regulon function in viper package by Keith Hughitt ▴ 130
Hi, I'm afraid not, so I don't think I can be much help, unfortunately. In the past, the authors of ARACNe-AP were generally quite responsi…
Comment: Data input for aracne2regulon function in viper package by Luna_P • 0
Hello Keith, I am currently trying to use my ARACNE-AP generated networks in Viper. I did all three steps you mentioned above but my prob…
Answer: DESeq2 for allele-specific expression with contrasts between conditions by Michael Love 33k
There is a section in the vignette on interactions that will help you here. You want to test for within-individual effects (`allele`) and c…
Answer: Issues with Tximport by Michael Love 33k
Your file has no version numbers, while your `tx2gene` does have version numbers. While the names look similar, they are not a match. tximp…
Answer: Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() w by Michael Love 33k
This is fine and ignorable, it is coming from upstream packages: our use of a TxDb object to pull out transcript to gene mappings.
Votes
Comment: DESeq2: NA's in mcols(object)$betaConv
Answer: Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() w
simultaneous use of robust and weighting methods in limma
simultaneous use of robust and weighting methods in limma
Answer: RUVSeq and Salmon
Awards • All
Popular Question to Keith Hughitt ▴ 130
Scholar to Aaron Lun ★ 26k
Teacher to Martin Morgan 25k
Teacher to alexvpickering ▴ 110
Popular Question to k.vitting.seerup ▴ 100
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