Showing : AnnotationHub • reset
0
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479
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Help using reduceSimMatrix with a custom annotation
AnnotationHub GOSemSim rrvgo
updated 8 days ago by ▴ 80 • written 5 months ago by • 0
1
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3
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895
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac AnnotationHub
written 7 weeks ago by ▴ 110
5
votes
13
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2.0k
views
Installing annotation package in locally
AnnotationDbi AnnotationHub Annotation AnnotationForge
6 months ago KABILAN • 0
0
votes
3
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1.2k
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
8 months ago Anna • 0
1
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5
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1.5k
views
EnsDb: bad_weak_ptr
AnnotationHub BiocFileCache
10 months ago Lluís Revilla Sancho ▴ 760
0
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5
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1.7k
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Cannot connect to annotationhub server
AnnotationHub ExperimentHub
updated 10 months ago by 4.1k • written 10 months ago by • 0
0
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0
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409
views
News: AnnotationHub and ExperimentHub Access Downtime
AnnotationHub ExperimentHub
10 months ago shepherl 4.1k
1
vote
1
reply
502
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub ExperimentHub
updated 11 months ago by 68k • written 11 months ago by • 0
6
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12
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7.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
18 months ago • updated 12 months ago shepherl 4.1k
10
votes
41
replies
8.5k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 11 months ago by • 0 • written 6.4 years ago by ★ 4.1k
1
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6
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1.3k
views
unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 12 months ago by ▴ 230 • written 13 months ago by • 0
2
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1
reply
964
views
clusterProfiler, AnnotationHub, and discrepancies in GO Terms
Atlanticsalmon clusterPro Salmosalar AnnotationHub GeneOntology
updated 14 months ago by 43k • written 14 months ago by • 0
0
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0
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539
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Annotatr Duplicate Entries
annotatr AnnotationHub
15 months ago hayleyw • 0
2
votes
28
replies
6.3k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 17 months ago by 68k • written 2.4 years ago by ▴ 10
3
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4
replies
2.5k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 18 months ago by ★ 4.1k • written 18 months ago by • 0
1
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2
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1.2k
views
AnnotationHub data for Mus musculus seems to be missing, while previously it was there
tximeta AnnotationHub AnnotationHubData
18 months ago Thon • 0
0
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1
reply
1.0k
views
multiGSEA package in R not appropriately assigning metabolites to pathways?
metaboliteIDmapping AnnotationHub multiGSEA
2.3 years ago • updated 2.2 years ago Thomas • 0
2
votes
2
replies
1.1k
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
2.7 years ago Lenny186 • 0
0
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3
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2.2k
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub org.Hs.eg.db ensembldb
2.8 years ago • updated 2.7 years ago sandmann.t ▴ 70
9
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21
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16k
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 2.8 years ago by ▴ 10 • written 4.5 years ago by ▴ 40
0
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2
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2.4k
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AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub Install
updated 3.1 years ago by 4.1k • written 3.1 years ago by ▴ 70
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4
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1.7k
views
AnnotationHub
AnnotationHub
3.1 years ago junliqilinpan • 0
4
votes
6
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3.6k
views
OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)
AnnotationHub OrganismDbi org.Hs.eg.db
updated 3.2 years ago by 52k • written 3.2 years ago by • 0
9
votes
14
replies
8.8k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 9 months ago by 4.1k • written 3.3 years ago by ▴ 40
0
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2
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1.5k
views
AnnotationHub problem
AnnotationHub
3.3 years ago Jianxuan • 0
4
votes
8
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2.7k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
3.4 years ago • updated 3.0 years ago nattzy94 ▴ 20
1
vote
3
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1.7k
views
How delete the AnnotationHub downloaded datasets
AnnotationHub
updated 3.5 years ago by ★ 6.6k • written 3.5 years ago by • 0
2
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10
replies
3.2k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 3.5 years ago by ★ 4.1k • written 3.5 years ago by • 0
0
votes
0
replies
800
views
LRBaseDbi error
LRBaseDbi AnnotationHub
3.7 years ago Francois Marchildon ▴ 20
1
vote
2
replies
2.2k
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb Bioconductor AnnotationHub clusterProfiler
updated 4.0 years ago by ★ 4.1k • written 4.0 years ago by • 0
0
votes
1
reply
1.5k
views
News: Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache AnnotationHub ExperimentHub cache
4.1 years ago shepherl 4.1k
0
votes
3
replies
5.9k
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub biomaRt
updated 2.7 years ago by • 0 • written 4.1 years ago by ▴ 20
3
votes
11
replies
6.9k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 15 months ago by ★ 4.1k • written 4.2 years ago by • 0
11
votes
13
replies
5.8k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
4.4 years ago • updated 4.3 years ago rohitsatyam102 ▴ 20
3
votes
2
replies
2.6k
views
Issue with AnnotationHub
AnnotationHub
4.4 years ago rahnaman ▴ 10
1
vote
2
replies
1.6k
views
How to mimic biomaRt results with AnnotationHub?
biomaRt AnnotationHub
4.5 years ago Ezgi ▴ 60
1
vote
3
replies
1.4k
views
AnnotationHub: failed to load resource name
AnnotationHub
4.7 years ago ben.ponv • 0
4
votes
17
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3.4k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by ▴ 10
4
votes
2
replies
2.2k
views
News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
4.7 years ago Johannes Rainer ★ 2.1k
8
votes
16
replies
8.8k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 4.7 years ago by 4.1k • written 4.7 years ago by ▴ 680
0
votes
2
replies
1.8k
views
Can't select GO from AnnotationHub orgDB packages
GO.db AnnotationHub OrgDB
updated 4.8 years ago by 68k • written 4.8 years ago by ★ 2.0k
0
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3
replies
1.5k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 670
3
votes
6
replies
3.1k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 2.8 years ago by 4.1k • written 5.0 years ago by ★ 2.0k
2
votes
8
replies
2.4k
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error enrichGO annotationHub clusterProfiler Job
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
1
vote
5
replies
2.2k
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 5.1 years ago by 4.1k • written 5.1 years ago by • 0
0
votes
2
replies
1.4k
views
hg38 tracks for AnnotationHub
annotationhub
5.2 years ago Michael Love 43k
0
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1
reply
1.2k
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 5.2 years ago by 4.1k • written 5.2 years ago by • 0
0
votes
8
replies
3.5k
views
I can't use AnnotationHub()
AnnotationHub
5.3 years ago 755606975 • 0
1
vote
3
replies
2.8k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub Ensembl Mouse AnnotationHub Ensembl
5.4 years ago dmgatti ▴ 10
3
votes
0
replies
1.6k
views
News: EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation ensembldb EnsDb AnnotationHub News
5.4 years ago Johannes Rainer ★ 2.1k
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an by James W. MacDonald 68k
Have you figured out how to do this using tidy grammar? Using non-tidy grammar is quite simple, and perhaps you already know how to do that…
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You can use [bioc-run][1] to simplify things as well. [1]: https://github.com/Bioconductor/bioc-run/tree/devel
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You show how you modified the container, but not how you are running it, which is the critical part.
Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your reply. > Per sample all counts are scaled by the same size factor so I strongly assume that something was parsed here …
Comment: Discrepancies in normalised count data vs unnormalised by ATpoint ★ 4.8k
Please show examples using `plotCounts()`. Custom spreadsheets harbor the risk of parsing errors along the way which very often explains wh…
Votes
Answer: How to combine two DESeq2 objects (dds) for analysis
How to combine two DESeq2 objects (dds) for analysis
How can I correctly use phyloseq with Docker?
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
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