Showing : Annotationhub • reset
2
votes
2
replies
147
views
Failure to download resources (MeSHDb) from AnnotationHub
MeSHDb AnnotationHub
4 weeks ago Steve Lianoglou ★ 13k
3
votes
3
replies
645
views
AnnotationHub/ExperimentHub resources backup
AnnotationHub HubPub ExperimentHub
updated 6 months ago by 68k • written 6 months ago by ▴ 50
0
votes
1
reply
700
views
Help using reduceSimMatrix with a custom annotation
AnnotationHub GOSemSim rrvgo
updated 7 months ago by ▴ 80 • written 13 months ago by • 0
1
vote
3
replies
1.2k
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac AnnotationHub
written 9 months ago by ▴ 110
5
votes
13
replies
2.4k
views
Installing annotation package in locally
AnnotationDbi AnnotationHub Annotation AnnotationForge
13 months ago KABILAN • 0
0
votes
3
replies
1.5k
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
16 months ago Anna • 0
1
vote
5
replies
2.1k
views
EnsDb: bad_weak_ptr
AnnotationHub BiocFileCache
17 months ago Lluís Revilla Sancho ▴ 760
0
votes
5
replies
2.1k
views
Cannot connect to annotationhub server
AnnotationHub ExperimentHub
updated 17 months ago by 4.2k • written 17 months ago by • 0
0
votes
0
replies
675
views
News: AnnotationHub and ExperimentHub Access Downtime
AnnotationHub ExperimentHub
17 months ago shepherl 4.2k
1
vote
1
reply
702
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub ExperimentHub
updated 18 months ago by 68k • written 18 months ago by • 0
6
votes
12
replies
8.6k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
2.1 years ago • updated 19 months ago shepherl 4.2k
10
votes
41
replies
10k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 18 months ago by • 0 • written 7.0 years ago by ★ 4.1k
1
vote
6
replies
1.8k
views
unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 20 months ago by ▴ 230 • written 20 months ago by • 0
2
votes
1
reply
1.2k
views
clusterProfiler, AnnotationHub, and discrepancies in GO Terms
Atlanticsalmon clusterPro Salmosalar AnnotationHub GeneOntology
updated 21 months ago by 43k • written 21 months ago by • 0
0
votes
1
reply
673
views
Annotatr Duplicate Entries
annotatr AnnotationHub
written 22 months ago by • 0
2
votes
28
replies
7.2k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 2.0 years ago by 68k • written 3.0 years ago by ▴ 10
3
votes
4
replies
2.9k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 2.1 years ago by ★ 4.1k • written 2.1 years ago by • 0
1
vote
2
replies
1.5k
views
AnnotationHub data for Mus musculus seems to be missing, while previously it was there
tximeta AnnotationHub AnnotationHubData
2.1 years ago Thon • 0
0
votes
1
reply
1.2k
views
multiGSEA package in R not appropriately assigning metabolites to pathways?
metaboliteIDmapping AnnotationHub multiGSEA
2.9 years ago • updated 2.8 years ago Thomas • 0
2
votes
2
replies
1.2k
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
3.3 years ago Lenny186 • 0
0
votes
3
replies
2.6k
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub org.Hs.eg.db ensembldb
3.4 years ago • updated 3.3 years ago sandmann.t ▴ 70
9
votes
21
replies
17k
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 3.4 years ago by ▴ 10 • written 5.1 years ago by ▴ 40
0
votes
2
replies
2.6k
views
AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub Install
updated 3.7 years ago by 4.2k • written 3.7 years ago by ▴ 70
0
votes
4
replies
2.0k
views
AnnotationHub
AnnotationHub
3.7 years ago junliqilinpan • 0
4
votes
6
replies
4.0k
views
OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)
AnnotationHub OrganismDbi org.Hs.eg.db
updated 3.8 years ago by 53k • written 3.8 years ago by • 0
9
votes
14
replies
10k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 16 months ago by 4.2k • written 3.9 years ago by ▴ 40
0
votes
2
replies
1.7k
views
AnnotationHub problem
AnnotationHub
3.9 years ago Jianxuan • 0
4
votes
8
replies
3.1k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
4.0 years ago • updated 3.6 years ago nattzy94 ▴ 20
1
vote
3
replies
2.0k
views
How delete the AnnotationHub downloaded datasets
AnnotationHub
updated 4.1 years ago by ★ 6.6k • written 4.1 years ago by • 0
2
votes
10
replies
3.6k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 4.1 years ago by ★ 4.1k • written 4.1 years ago by • 0
0
votes
0
replies
903
views
LRBaseDbi error
LRBaseDbi AnnotationHub
4.3 years ago Francois Marchildon ▴ 20
1
vote
2
replies
2.6k
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb Bioconductor AnnotationHub clusterProfiler
updated 4.6 years ago by ★ 4.1k • written 4.6 years ago by • 0
0
votes
1
reply
1.7k
views
News: Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache AnnotationHub ExperimentHub cache
4.7 years ago shepherl 4.2k
0
votes
3
replies
6.9k
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub biomaRt
updated 3.3 years ago by • 0 • written 4.7 years ago by ▴ 20
3
votes
11
replies
7.7k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 22 months ago by ★ 4.1k • written 4.8 years ago by • 0
11
votes
13
replies
6.5k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
5.0 years ago • updated 4.9 years ago rohitsatyam102 ▴ 20
3
votes
2
replies
2.8k
views
Issue with AnnotationHub
AnnotationHub
5.0 years ago rahnaman ▴ 10
1
vote
2
replies
1.7k
views
How to mimic biomaRt results with AnnotationHub?
biomaRt AnnotationHub
5.1 years ago Ezgi ▴ 60
1
vote
3
replies
1.6k
views
AnnotationHub: failed to load resource name
AnnotationHub
5.3 years ago ben.ponv • 0
4
votes
17
replies
3.8k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by ▴ 10
4
votes
2
replies
2.4k
views
News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
5.3 years ago Johannes Rainer ★ 2.1k
8
votes
16
replies
9.5k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 5.3 years ago by 4.2k • written 5.3 years ago by ▴ 680
0
votes
2
replies
2.0k
views
Can't select GO from AnnotationHub orgDB packages
GO.db AnnotationHub OrgDB
updated 5.4 years ago by 68k • written 5.4 years ago by ★ 2.0k
0
votes
3
replies
1.7k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 670
3
votes
6
replies
3.4k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 3.4 years ago by 4.2k • written 5.6 years ago by ★ 2.0k
2
votes
8
replies
2.8k
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error enrichGO annotationHub clusterProfiler Job
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
1
vote
5
replies
2.5k
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 5.7 years ago by 4.2k • written 5.7 years ago by • 0
0
votes
2
replies
1.5k
views
hg38 tracks for AnnotationHub
annotationhub
5.8 years ago Michael Love 43k
0
votes
1
reply
1.4k
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 5.8 years ago by 4.2k • written 5.8 years ago by • 0
0
votes
8
replies
3.9k
views
I can't use AnnotationHub()
AnnotationHub
5.9 years ago 755606975 • 0
131 results • Page 1 of 3
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.2k
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