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Showing :
AnnotationHub
•
reset
0
votes
1
reply
47
views
News:
Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache
AnnotationHub
ExperimentHub
cache
4 days ago • updated 2 days ago
shepherl
2.6k
0
votes
2
replies
79
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub
biomaRt
17 days ago • updated 15 days ago
rohitsatyam102
▴ 10
1
vote
2
replies
135
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 9 weeks ago by
Guido Hooiveld
★ 2.9k • written 9 weeks ago by
Alberto
• 0
11
votes
13
replies
496
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic
AnnotationHub
GenomicRanges
org.Hs.eg.db
4 months ago • updated 9 weeks ago
rohitsatyam102
▴ 10
5
votes
20
replies
4.6k
views
ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tb…
AnnotationHub
dplyr
5 months ago • updated 7 weeks ago
georgia.katsoula
▴ 10
3
votes
2
replies
315
views
Issue with AnnotationHub
AnnotationHub
4 months ago
rahnaman
▴ 10
1
vote
2
replies
131
views
How to mimic biomaRt results with AnnotationHub?
biomaRt
AnnotationHub
4 months ago
Ezgi
▴ 30
1
vote
3
replies
111
views
AnnotationHub: failed to load resource name
AnnotationHub
7 months ago
ben.ponv
• 0
4
votes
17
replies
385
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt
annotation
Ensembl
annotationHub
updated 7 months ago by
Kevin Blighe
2.7k • written 7 months ago by
Didi
▴ 10
4
votes
2
replies
164
views
News:
ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb
ensembldb
annotation
AnnotationHub
News
7 months ago
Johannes Rainer
★ 1.8k
7
votes
16
replies
471
views
Cannot connect to ExperimentHub server
ExperimentHub
AnnotationHub
SingleR
updated 8 months ago by
shepherl
2.6k • written 8 months ago by
enricoferrero
▴ 570
0
votes
2
replies
128
views
Can't select GO from AnnotationHub orgDB packages
GO.db
AnnotationHub
OrgDB
updated 8 months ago by
James W. MacDonald
56k • written 8 months ago by
Jenny Drnevich
★ 2.0k
0
votes
3
replies
122
views
extracting the genes associated with a specific pathway
pathway
KEGG
annotation
annotationhub
updated 10 months ago by
James W. MacDonald
56k • written 10 months ago by
Bogdan
▴ 610
1
vote
4
replies
102
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub
OrgDb
snapshotDate
updated 10 months ago by
shepherl
2.6k • written 10 months ago by
Jenny Drnevich
★ 2.0k
2
votes
8
replies
196
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error
enrichGO
annotationHub
clusterProfiler
Job
updated 11 months ago by
James W. MacDonald
56k • written 11 months ago by
bnajafpour
• 0
1
vote
5
replies
126
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 12 months ago by
shepherl
2.6k • written 12 months ago by
dilaik
• 0
0
votes
2
replies
70
views
hg38 tracks for AnnotationHub
annotationhub
13 months ago
Michael Love
32k
0
votes
1
reply
75
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub
Shiny
Rstudio
updated 13 months ago by
shepherl
2.6k • written 13 months ago by
bwiley4
• 0
0
votes
8
replies
366
views
I can't use AnnotationHub()
AnnotationHub
15 months ago
755606975
• 0
1
vote
3
replies
533
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub
Ensembl
Mouse
AnnotationHub Ensembl
16 months ago
dmgatti
▴ 10
3
votes
0
replies
197
views
News:
EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation
ensembldb
EnsDb
AnnotationHub
News
16 months ago
Johannes Rainer
★ 1.8k
0
votes
2
replies
209
views
how to choose annotation file in AnnotationHub web server
annotation
AnnotationHub
16 months ago
15958021290
▴ 10
3
votes
4
replies
165
views
Are AH52264, AH66175, and AH70594 duplicates?
AnnotationHub
updated 18 months ago by
shepherl
2.6k • written 18 months ago by
Aditya
▴ 120
1
vote
3
replies
175
views
Problem with AnnotationHub after crash during first download of metadata
AnnotationHub
updated 19 months ago by
shepherl
2.6k • written 19 months ago by
konstantinos.bogias
▴ 10
7
votes
44
replies
895
views
OrgDB download failed via AnnotationHub
annotationhub
orgdb
updated 21 months ago by
shepherl
2.6k • written 22 months ago by
chirag.parsania
• 0
2
votes
0
replies
228
views
News:
ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
updated 23 months ago by
nguyenlieuduoc
• 0 • written 23 months ago by
shepherl
2.6k
1
vote
4
replies
203
views
AnnotationHub Server denied you to change the given directory
annotation
annotationhub
updated 23 months ago by
shepherl
2.6k • written 23 months ago by
bastien.ducreux
▴ 10
0
votes
11
replies
378
views
AH134 and other AnnotationHub objects unavailable as "defunct"
AnnotationHub
updated 23 months ago by
shepherl
2.6k • written 23 months ago by
Robert K. Bradley
▴ 40
1
vote
1
reply
232
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
24 months ago
wecai
• 0
3
votes
9
replies
2.3k
views
AnnotationHub corrupt database
annotationhub
updated 2.1 years ago by
shepherl
2.6k • written 5.7 years ago by
Koen Van den Berge
▴ 180
0
votes
0
replies
256
views
News:
ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub
annotationdata
ensembl
gtf
2bit
News
2.1 years ago
shepherl
2.6k
5
votes
10
replies
736
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 3 months ago by
Johannes Rainer
★ 1.8k • written 2.4 years ago by
Guido Hooiveld
★ 2.9k
1
vote
7
replies
398
views
News:
ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
2.5 years ago
shepherl
2.6k
0
votes
5
replies
399
views
annotationhub: data update
annotationhub
updated 2.7 years ago by
shepherl
2.6k • written 2.7 years ago by
Kasper Daniel Hansen
6.5k
0
votes
0
replies
356
views
News:
ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub
ensembl
gtf
2bit
annotationdata
News
2.7 years ago
shepherl
2.6k
1
vote
2
replies
507
views
AnnotationHub, force update snapshot date?
annotationhub
updated 2.7 years ago by
shepherl
2.6k • written 2.7 years ago by
Vang Le
▴ 70
5
votes
4
replies
531
views
Eliminating repetitive calls to ExperimentHub
experimenthub
annotationhub
large dataset
2.9 years ago
slinker
▴ 20
0
votes
6
replies
557
views
initialization of AnnotationHub() in version 2.12.0 is problematically verbose
AnnotationHub
updated 2.9 years ago by
Martin Morgan
25k • written 2.9 years ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
400
views
News:
ensembl 92 gtfs and fasta twobits have been added to AnnotationHub
ensembl
gtf
2bit
annotationhub
News
3.0 years ago
shepherl
2.6k
1
vote
0
replies
732
views
News:
ensembl 91 gtfs and fasta twobits have been added to AnnotationHub
annotationhub
ensembl
gtf
2bit
News
3.3 years ago
shepherl
2.6k
0
votes
1
reply
571
views
News:
OrgDbs in AnnotationHub
annotationhub
orgdb
News
3.4 years ago
shepherl
2.6k
0
votes
0
replies
514
views
News:
OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb
txdb
bioconductor
annotation
annotationhub
News
3.5 years ago
shepherl
2.6k
0
votes
2
replies
461
views
Trouble loading Roadmap data from AnnotationHub
annotationhub
updated 3.5 years ago by
shepherl
2.6k • written 3.5 years ago by
bletteb18
• 0
1
vote
0
replies
666
views
Error: failed to load resource reason: invalid class GRanges object: seqnames(x) contains missing values for newer GRCh38 annotations
AnnotationHub
3.5 years ago
marcel.schilling
▴ 10
0
votes
2
replies
482
views
AnnotationHub downloading dataset fail
annotationhub
download_error
updated 3.6 years ago by
James W. MacDonald
56k • written 3.6 years ago by
vitay.dora
• 0
4
votes
10
replies
644
views
Suggestion: spinning wheel for AnnotationHub
annotationhub
updated 3.6 years ago by
shepherl
2.6k • written 3.6 years ago by
Michael Love
32k
0
votes
1
reply
614
views
querying annotation hub for common TF, in common cell line returns no results....
annotate
annotationhub
updated 3.6 years ago by
shepherl
2.6k • written 3.6 years ago by
chrisclarkson100
▴ 50
1
vote
0
replies
782
views
News:
ensembl 90 ensembldb EnsDb databases have been added to AnnotationHub
ensemblb
ensembl
AnnotationHub
annotation
News
3.6 years ago
Johannes Rainer
★ 1.8k
1
vote
0
replies
606
views
News:
ensembl 90 gtfs and fasta twobits have been added to AnnotationHub
annotationhub
bioconductor
News
updated 3.6 years ago by
Martin Morgan
25k • written 3.6 years ago by
shepherl
2.6k
0
votes
6
replies
697
views
Why are important organisms missing from AnnotationHub. Example query(hub, "Zea")
orgdb
annotationhub
3.7 years ago
slbai01
• 0
101 results • Page
1 of 3
Recent ...
Replies
Answer: Differential Transcript Usage: complex factorial design
by
Gordon Smyth
42k
edgeR does differential expression for transcripts via the catchSalmon function followed the usual edgeR pipelines as you would do for gene…
Comment: RSamtools idxstatsBam not working with remote bam file
by
mja18
▴ 30
Thanks Martin. Yes, that works.
Answer: RSamtools idxstatsBam not working with remote bam file
by
Martin Morgan
25k
Can you tell me if the following works for you? In a new R session ```{r} library(Rsamtools) setMethod(idxstatsBam, "BamFile", …
Comment: Aspli: error with gbCounts
by
achernomoretz
• 0
Hi Jeremy. We got it and we are working on the issue. Thanks for your patience. A
Comment: Aspli: error with gbCounts
by
jbono
• 0
Sorry, I forgot to respond here that I sent the file via email. Please let me know if you didn't receive it, thanks!
Votes
Answer: RSamtools idxstatsBam not working with remote bam file
Running > 100 samples per group - memory issues
R failing to load genome files from EnsDb.Hsapiens.v86
Comment: TCGA data analysis
Comment: BSGenome Forge for non-model organism
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