Showing : annotationhub • reset
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39
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LRBaseDbi error
LRBaseDbi AnnotationHub
15 days ago Francois Marchildon ▴ 20
1
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2
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237
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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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192
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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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453
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Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub biomaRt
6 months ago rohitsatyam102 ▴ 20
1
vote
2
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396
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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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821
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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
views
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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525
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Issue with AnnotationHub
AnnotationHub
9 months ago rahnaman ▴ 10
1
vote
2
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237
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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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231
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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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700
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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
votes
2
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331
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News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
13 months ago Johannes Rainer ★ 1.9k
8
votes
16
replies
992
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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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231
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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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232
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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
vote
4
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234
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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
votes
8
replies
323
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gene enrichment using enrichGO function throuth annotationHub orgDb
software error enrichGO annotationHub clusterProfiler Job
updated 17 months ago by 58k • written 17 months ago by • 0
1
vote
5
replies
260
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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149
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hg38 tracks for AnnotationHub
annotationhub
18 months ago Michael Love 34k
0
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1
reply
173
views
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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598
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I can't use AnnotationHub()
AnnotationHub
20 months ago 755606975 • 0
1
vote
3
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847
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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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312
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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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324
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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
vote
3
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257
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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
votes
44
replies
1.3k
views
OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 2.2 years ago by 2.8k • written 2.3 years ago by • 0
2
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0
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321
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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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291
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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577
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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
347
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
2.4 years ago wecai • 0
3
votes
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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364
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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
992
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
replies
493
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
494
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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433
views
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
634
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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658
views
Eliminating repetitive calls to ExperimentHub
experimenthub annotationhub large dataset
3.4 years ago slinker ▴ 20
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6
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682
views
initialization of AnnotationHub() in version 2.12.0 is problematically verbose
AnnotationHub
updated 3.4 years ago by 25k • written 3.4 years ago by ▴ 40
0
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0
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524
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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
807
views
News: ensembl 91 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit News
3.8 years ago shepherl 2.8k
0
votes
1
reply
657
views
News: OrgDbs in AnnotationHub
annotationhub orgdb News
3.8 years ago shepherl 2.8k
0
votes
0
replies
601
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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
votes
2
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548
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
replies
750
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
votes
2
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549
views
AnnotationHub downloading dataset fail
annotationhub download_error
updated 4.0 years ago by 58k • written 4.0 years ago by • 0
4
votes
10
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722
views
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
693
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
vote
0
replies
852
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News: ensembl 90 ensembldb EnsDb databases have been added to AnnotationHub
ensemblb ensembl AnnotationHub annotation News
4.1 years ago Johannes Rainer ★ 1.9k
50 results • Page 1 of 1
Recent ...
Replies
Comment: Returning to edgeR version 3.26.1? by mvanhorn • 0
Thank you very much for your reply! Our project is a reanalysis of large sets of RNA-seq data to identify circular RNAs using the CIRIquan…
Comment: "full model matrix is less than full rank" by ATpoint ▴ 840
My best guess is that young and old are not "young" or "old" but include some hidden whitespaces like " young" or "old ". That would then m…
Answer: Reading vcf file with readVcf by James W. MacDonald 58k
Usually when you run out of RAM, you usually get an error saying that 'R couldn't allocate a vector of size <some number>'. When it just sa…
Answer: Genic annotations of whole hg38 by James W. MacDonald 58k
What exactly do you mean by 'proportion of genic annotations'? One possibility would be to see what proportion of all the exons are covered…
Answer: Understanding output of Negative Binomial in DESeq2 by Michael Love 34k
> Does this mean that there are seven genes in total that will have significant adjusted p-value? yes > i recall when multiple linea…
Votes
simultaneous use of robust and weighting methods in limma
simultaneous use of robust and weighting methods in limma
Answer: Swish direction of comparison based on order of factors
Comment: Gradient dotplot
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
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