Showing : annotationhub • reset
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30
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LRBaseDbi error
LRBaseDbi AnnotationHub
10 days ago Francois Marchildon ▴ 20
1
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2
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230
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Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb Bioconductor AnnotationHub clusterProfiler
updated 4 months ago by ★ 3.0k • written 4 months ago by • 0
0
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1
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188
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News: Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache AnnotationHub ExperimentHub cache
5 months ago shepherl 2.8k
0
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2
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443
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Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub biomaRt
5 months ago rohitsatyam102 ▴ 20
1
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2
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389
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GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 7 months ago by ★ 3.0k • written 7 months ago by • 0
11
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13
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819
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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
9 months ago • updated 7 months ago rohitsatyam102 ▴ 20
5
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20
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7.6k
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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
10 months ago • updated 8 weeks ago georgia.katsoula ▴ 10
3
votes
2
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522
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Issue with AnnotationHub
AnnotationHub
9 months ago rahnaman ▴ 10
1
vote
2
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233
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How to mimic biomaRt results with AnnotationHub?
biomaRt AnnotationHub
10 months ago Ezgi ▴ 30
1
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3
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226
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AnnotationHub: failed to load resource name
AnnotationHub
12 months ago ben.ponv • 0
4
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17
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693
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annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 12 months ago by 3.4k • written 12 months ago by ▴ 10
4
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2
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322
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News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
12 months ago Johannes Rainer ★ 1.9k
8
votes
16
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980
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Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 13 months ago by 2.8k • written 13 months ago by ▴ 570
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2
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229
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Can't select GO from AnnotationHub orgDB packages
GO.db AnnotationHub OrgDB
updated 14 months ago by 58k • written 14 months ago by ★ 2.0k
0
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3
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229
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extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 15 months ago by 58k • written 15 months ago by ▴ 620
1
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4
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232
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How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 16 months ago by 2.8k • written 16 months ago by ★ 2.0k
2
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8
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319
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gene enrichment using enrichGO function throuth annotationHub orgDb
software error enrichGO annotationHub clusterProfiler Job
updated 16 months ago by 58k • written 16 months ago by • 0
1
vote
5
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258
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 17 months ago by 2.8k • written 17 months ago by • 0
0
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2
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148
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hg38 tracks for AnnotationHub
annotationhub
18 months ago Michael Love 34k
0
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1
reply
169
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AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 18 months ago by 2.8k • written 18 months ago by • 0
0
votes
8
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590
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I can't use AnnotationHub()
AnnotationHub
20 months ago 755606975 • 0
1
vote
3
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842
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AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub Ensembl Mouse AnnotationHub Ensembl
21 months ago dmgatti ▴ 10
3
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0
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273
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News: EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation ensembldb EnsDb AnnotationHub News
22 months ago Johannes Rainer ★ 1.9k
0
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2
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308
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how to choose annotation file in AnnotationHub web server
annotation AnnotationHub
22 months ago 15958021290 ▴ 10
3
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4
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320
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Are AH52264, AH66175, and AH70594 duplicates?
AnnotationHub
updated 23 months ago by 2.8k • written 23 months ago by ▴ 120
1
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3
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250
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Problem with AnnotationHub after crash during first download of metadata
AnnotationHub
updated 2.0 years ago by 2.8k • written 2.1 years ago by ▴ 10
7
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44
replies
1.3k
views
OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 2.2 years ago by 2.8k • written 2.2 years ago by • 0
2
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0
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315
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News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 2.4 years ago by • 0 • written 2.4 years ago by 2.8k
1
vote
4
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281
views
AnnotationHub Server denied you to change the given directory
annotation annotationhub
updated 2.4 years ago by 2.8k • written 2.4 years ago by ▴ 10
0
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11
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574
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AH134 and other AnnotationHub objects unavailable as "defunct"
AnnotationHub
updated 2.4 years ago by 2.8k • written 2.4 years ago by ▴ 40
1
vote
1
reply
340
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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
2.4 years ago wecai • 0
3
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9
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2.5k
views
AnnotationHub corrupt database
annotationhub
updated 2.5 years ago by 2.8k • written 6.1 years ago by ▴ 180
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0
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357
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News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
2.6 years ago shepherl 2.8k
5
votes
10
replies
988
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 8 months ago by ★ 1.9k • written 2.8 years ago by ★ 3.0k
1
vote
7
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491
views
News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
2.9 years ago shepherl 2.8k
0
votes
5
replies
491
views
annotationhub: data update
annotationhub
updated 3.1 years ago by 2.8k • written 3.1 years ago by 6.5k
0
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0
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432
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News: ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit annotationdata News
3.1 years ago shepherl 2.8k
1
vote
2
replies
632
views
AnnotationHub, force update snapshot date?
annotationhub
updated 3.2 years ago by 2.8k • written 3.2 years ago by ▴ 70
5
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4
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656
views
Eliminating repetitive calls to ExperimentHub
experimenthub annotationhub large dataset
3.3 years ago slinker ▴ 20
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6
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679
views
initialization of AnnotationHub() in version 2.12.0 is problematically verbose
AnnotationHub
updated 3.3 years ago by 25k • written 3.4 years ago by ▴ 40
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0
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523
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News: ensembl 92 gtfs and fasta twobits have been added to AnnotationHub
ensembl gtf 2bit annotationhub News
3.4 years ago shepherl 2.8k
1
vote
0
replies
805
views
News: ensembl 91 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit News
3.7 years ago shepherl 2.8k
0
votes
1
reply
655
views
News: OrgDbs in AnnotationHub
annotationhub orgdb News
3.8 years ago shepherl 2.8k
0
votes
0
replies
599
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News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
3.9 years ago shepherl 2.8k
0
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2
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547
views
Trouble loading Roadmap data from AnnotationHub
annotationhub
updated 3.9 years ago by 2.8k • written 3.9 years ago by • 0
1
vote
0
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748
views
Error: failed to load resource reason: invalid class GRanges object: seqnames(x) contains missing values for newer GRCh38 annotations
AnnotationHub
3.9 years ago marcel.schilling ▴ 10
0
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2
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544
views
AnnotationHub downloading dataset fail
annotationhub download_error
updated 4.0 years ago by 58k • written 4.0 years ago by • 0
4
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10
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719
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Suggestion: spinning wheel for AnnotationHub
annotationhub
updated 4.0 years ago by 2.8k • written 4.1 years ago by 34k
0
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1
reply
691
views
querying annotation hub for common TF, in common cell line returns no results....
annotate annotationhub
updated 4.0 years ago by 2.8k • written 4.0 years ago by ▴ 50
1
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0
replies
849
views
News: ensembl 90 ensembldb EnsDb databases have been added to AnnotationHub
ensemblb ensembl AnnotationHub annotation News
4.0 years ago Johannes Rainer ★ 1.9k
50 results • Page 1 of 1
Recent ...
Replies
Comment: Recalculated abundance data output table with DEseq2 by Michael Love 34k
Yes, DESeq() then results(). When you print the table it will say MLE. No we don’t have a function to do that.
Comment: Recalculated abundance data output table with DEseq2 by michael.morash • 0
Thanks for getting back to me so quickly. The final comparison we are looking to report are the effects of filtering out low count genes us…
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Field -Ye • 0
Hi Professor Smyth, Thank you for pointing me to your previous publication. I went through the verbal part and found you did pursue the DG…
Comment: Macbook M1 install genefilter failed by Michael Love 34k
Try [n] to updating packages, and "no" to install from source.
Comment: Macbook M1 install genefilter failed by Alexandre • 0
Hi Michael, Sure > BiocManager::install("DESeq2") 'getOption("repos")' replaces Bioconductor standard repositories, see '?re…
Votes
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
Comment: How to build a GRangesList where each GRanges element is a CDS coordinate of gen
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