Showing : annotationHub • reset
7
votes
25
replies
3.5k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 13 days ago by • 0 • written 4.8 years ago by ★ 3.7k
0
votes
1
reply
454
views
multiGSEA package in R not appropriately assigning metabolites to pathways?
metaboliteIDmapping AnnotationHub multiGSEA
8 months ago • updated 7 months ago Thomas • 0
0
votes
11
replies
1.1k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 9 months ago by 63k • written 9 months ago by • 0
2
votes
2
replies
510
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
13 months ago • updated 12 months ago Lenny186 • 0
0
votes
3
replies
714
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub org.Hs.eg.db ensembldb
13 months ago sandmann.t ▴ 70
9
votes
21
replies
13k
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 13 months ago by ▴ 10 • written 2.9 years ago by ▴ 40
0
votes
2
replies
1.5k
views
AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub Install
updated 18 months ago by 3.5k • written 18 months ago by • 0
0
votes
4
replies
780
views
AnnotationHub
AnnotationHub
18 months ago junliqilinpan • 0
4
votes
6
replies
1.5k
views
OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)
AnnotationHub OrganismDbi org.Hs.eg.db
updated 18 months ago by 48k • written 18 months ago by • 0
8
votes
9
replies
4.0k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 20 months ago by 16k • written 20 months ago by ▴ 40
0
votes
2
replies
636
views
AnnotationHub problem
AnnotationHub
20 months ago Jianxuan • 0
4
votes
8
replies
1.3k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
21 months ago • updated 16 months ago nattzy94 ▴ 20
1
vote
3
replies
841
views
How delete the AnnotationHub downloaded datasets
AnnotationHub
updated 23 months ago by ★ 6.1k • written 23 months ago by • 0
2
votes
10
replies
1.8k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 23 months ago by ★ 3.7k • written 23 months ago by • 0
0
votes
0
replies
435
views
LRBaseDbi error
LRBaseDbi AnnotationHub
2.0 years ago Francois Marchildon ▴ 20
1
vote
2
replies
1.0k
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb Bioconductor AnnotationHub clusterProfiler
updated 2.4 years ago by ★ 3.7k • written 2.4 years ago by • 0
0
votes
1
reply
819
views
News: Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache AnnotationHub ExperimentHub cache
2.5 years ago shepherl 3.5k
0
votes
3
replies
3.3k
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub biomaRt
updated 13 months ago by • 0 • written 2.5 years ago by ▴ 20
3
votes
9
replies
3.6k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 4 weeks ago by ▴ 10 • written 2.6 years ago by • 0
11
votes
13
replies
2.9k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
2.8 years ago • updated 2.6 years ago rohitsatyam102 ▴ 20
3
votes
2
replies
1.5k
views
Issue with AnnotationHub
AnnotationHub
2.8 years ago rahnaman ▴ 10
1
vote
2
replies
880
views
How to mimic biomaRt results with AnnotationHub?
biomaRt AnnotationHub
2.9 years ago Ezgi ▴ 60
1
vote
3
replies
739
views
AnnotationHub: failed to load resource name
AnnotationHub
3.1 years ago ben.ponv • 0
4
votes
17
replies
1.9k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 3.1 years ago by 3.8k • written 3.1 years ago by ▴ 10
4
votes
2
replies
1.2k
views
News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
3.1 years ago Johannes Rainer ★ 2.0k
8
votes
16
replies
4.0k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 3.1 years ago by 3.5k • written 3.1 years ago by ▴ 660
0
votes
2
replies
941
views
Can't select GO from AnnotationHub orgDB packages
GO.db AnnotationHub OrgDB
updated 3.2 years ago by 63k • written 3.2 years ago by ★ 2.0k
0
votes
3
replies
801
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 3.3 years ago by 63k • written 3.3 years ago by ▴ 660
3
votes
6
replies
1.6k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 14 months ago by 3.5k • written 3.3 years ago by ★ 2.0k
2
votes
8
replies
1.1k
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error enrichGO annotationHub clusterProfiler Job
updated 3.4 years ago by 63k • written 3.4 years ago by • 0
1
vote
5
replies
1.2k
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 3.5 years ago by 3.5k • written 3.5 years ago by • 0
0
votes
2
replies
700
views
hg38 tracks for AnnotationHub
annotationhub
3.6 years ago Michael Love 40k
0
votes
1
reply
686
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 3.6 years ago by 3.5k • written 3.6 years ago by • 0
0
votes
8
replies
1.9k
views
I can't use AnnotationHub()
AnnotationHub
3.7 years ago 755606975 • 0
1
vote
3
replies
1.9k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub Ensembl Mouse AnnotationHub Ensembl
3.8 years ago dmgatti ▴ 10
3
votes
0
replies
798
views
News: EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation ensembldb EnsDb AnnotationHub News
3.8 years ago Johannes Rainer ★ 2.0k
2
votes
2
replies
964
views
how to choose annotation file in AnnotationHub web server
annotation AnnotationHub
3.8 years ago 15958021290 ▴ 10
3
votes
4
replies
868
views
Are AH52264, AH66175, and AH70594 duplicates?
AnnotationHub
updated 3.9 years ago by 3.5k • written 3.9 years ago by ▴ 160
1
vote
3
replies
718
views
Problem with AnnotationHub after crash during first download of metadata
AnnotationHub
updated 4.0 years ago by 3.5k • written 4.1 years ago by ▴ 10
7
votes
44
replies
3.9k
views
OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 4.2 years ago by 3.5k • written 4.3 years ago by • 0
2
votes
0
replies
743
views
News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 4.4 years ago by • 0 • written 4.4 years ago by 3.5k
1
vote
4
replies
913
views
AnnotationHub Server denied you to change the given directory
annotation annotationhub
updated 4.4 years ago by 3.5k • written 4.4 years ago by ▴ 10
0
votes
11
replies
1.4k
views
AH134 and other AnnotationHub objects unavailable as "defunct"
AnnotationHub
updated 4.4 years ago by 3.5k • written 4.4 years ago by ▴ 40
1
vote
1
reply
828
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
4.4 years ago wecai • 0
3
votes
9
replies
3.5k
views
AnnotationHub corrupt database
annotationhub
updated 4.5 years ago by 3.5k • written 8.2 years ago by ▴ 180
0
votes
0
replies
769
views
News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
4.6 years ago shepherl 3.5k
1
vote
7
replies
862
views
News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
4.9 years ago shepherl 3.5k
0
votes
5
replies
955
views
annotationhub: data update
annotationhub
updated 5.1 years ago by 3.5k • written 5.1 years ago by 6.5k
0
votes
0
replies
766
views
News: ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit annotationdata News
5.1 years ago shepherl 3.5k
1
vote
2
replies
1.3k
views
AnnotationHub, force update snapshot date?
annotationhub
updated 5.2 years ago by 3.5k • written 5.2 years ago by ▴ 80
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Comment: List of Deprecated Packages for Bioc3.18 by Hervé Pagès 16k
Also the source package is not available [in BioC 3.17](https://bioconductor.org/packages/3.17/CancerInSilico) which means that the package…
Answer: DelayedArray::read_sparse_block by Hervé Pagès 16k
Hi Koki, Sorry again for the slow response. `read_sparse_block()` has been around for years. It's a generic function defined in the *…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Sorry for missing that one too. When writting blocks to an HDF5 file, the `write_block()` method for HDF5RealizationSink or TENxRealizatio…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Hi Koki, sorry for not seeing this before. > will SparseArraySeed in DelayedArray be replaced by this new sparse array format? Yes it wil…
Comment: Manual creation of qPCRset does not work by Ed Siefker ▴ 230
Thanks! This works for me.
Votes
Comment: List of Deprecated Packages for Bioc3.18
Answer: Manual creation of qPCRset does not work
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
Comment: comparing contrasts in edger/lima using makeContrasts function
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