Showing : Annotationhub • reset
2
votes
2
replies
119
views
Failure to download resources (MeSHDb) from AnnotationHub
MeSHDb AnnotationHub
9 days ago • updated 8 days ago Steve Lianoglou ★ 13k
3
votes
3
replies
624
views
AnnotationHub/ExperimentHub resources backup
AnnotationHub HubPub ExperimentHub
updated 6 months ago by 68k • written 6 months ago by ▴ 50
0
votes
1
reply
681
views
Help using reduceSimMatrix with a custom annotation
AnnotationHub GOSemSim rrvgo
updated 6 months ago by ▴ 80 • written 12 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 8 months ago by ▴ 110
5
votes
13
replies
2.4k
views
Installing annotation package in locally
AnnotationDbi AnnotationHub Annotation AnnotationForge
13 months ago • updated 12 months ago KABILAN • 0
0
votes
3
replies
1.5k
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
15 months ago Anna • 0
1
vote
5
replies
2.1k
views
EnsDb: bad_weak_ptr
AnnotationHub BiocFileCache
16 months ago Lluís Revilla Sancho ▴ 760
0
votes
5
replies
2.1k
views
Cannot connect to annotationhub server
AnnotationHub ExperimentHub
updated 16 months ago by 4.2k • written 17 months ago by • 0
0
votes
0
replies
662
views
News: AnnotationHub and ExperimentHub Access Downtime
AnnotationHub ExperimentHub
17 months ago shepherl 4.2k
1
vote
1
reply
689
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
8.5k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
2.1 years ago • updated 19 months ago shepherl 4.2k
10
votes
41
replies
10.0k
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
1.7k
views
unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 19 months ago by ▴ 230 • written 19 months ago by • 0
2
votes
1
reply
1.2k
views
clusterProfiler, AnnotationHub, and discrepancies in GO Terms
Atlanticsalmon clusterPro Salmosalar AnnotationHub GeneOntology
updated 20 months ago by 43k • written 20 months ago by • 0
0
votes
1
reply
667
views
Annotatr Duplicate Entries
annotatr AnnotationHub
written 21 months ago by • 0
2
votes
28
replies
7.1k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 23 months ago by 68k • written 2.9 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
1.4k
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
2.8 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
3.2 years ago Lenny186 • 0
0
votes
3
replies
2.5k
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub org.Hs.eg.db ensembldb
3.3 years ago • updated 3.2 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 3.3 years ago by ▴ 10 • written 5.0 years ago by ▴ 40
0
votes
2
replies
2.5k
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
1.9k
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 3.7 years ago by 53k • written 3.7 years ago by • 0
9
votes
14
replies
9.9k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 16 months ago by 4.2k • written 3.8 years ago by ▴ 40
0
votes
2
replies
1.7k
views
AnnotationHub problem
AnnotationHub
3.8 years ago Jianxuan • 0
4
votes
8
replies
3.0k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
3.9 years ago • updated 3.5 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
3.5k
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
895
views
LRBaseDbi error
LRBaseDbi AnnotationHub
4.2 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 4.5 years ago by ★ 4.1k • written 4.5 years ago by • 0
0
votes
1
reply
1.7k
views
News: Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache AnnotationHub ExperimentHub cache
4.6 years ago shepherl 4.2k
0
votes
3
replies
6.9k
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub biomaRt
updated 3.2 years ago by • 0 • written 4.6 years ago by ▴ 20
3
votes
11
replies
7.6k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 21 months ago by ★ 4.1k • written 4.8 years ago by • 0
11
votes
13
replies
6.4k
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 4.8 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
5.0 years ago Ezgi ▴ 60
1
vote
3
replies
1.6k
views
AnnotationHub: failed to load resource name
AnnotationHub
5.2 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 5.2 years ago by ★ 4.0k • written 5.2 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
5.2 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
1.9k
views
Can't select GO from AnnotationHub orgDB packages
GO.db AnnotationHub OrgDB
updated 5.3 years ago by 68k • written 5.3 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 3.3 years ago by 4.2k • written 5.5 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 5.5 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 5.6 years ago by 4.2k • written 5.6 years ago by • 0
0
votes
2
replies
1.5k
views
hg38 tracks for AnnotationHub
annotationhub
5.7 years ago Michael Love 43k
0
votes
1
reply
1.4k
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 5.7 years ago by 4.2k • written 5.7 years ago by • 0
0
votes
8
replies
3.9k
views
I can't use AnnotationHub()
AnnotationHub
5.8 years ago 755606975 • 0
131 results • Page 1 of 3
Recent ...
Replies
Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k
The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k
There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Votes
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Issues with downloading biomaRt - SeqInfo and S4 Vectors
Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
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