Showing : Annotationhub • reset
0
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122
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Help using reduceSimMatrix with a custom annotation
AnnotationHub GOSemSim rrvgo
5 weeks ago daccar98 • 0
5
votes
13
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1.6k
views
Installing annotation package in locally
AnnotationDbi AnnotationHub Annotation AnnotationForge
7 weeks ago KABILAN • 0
0
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3
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671
views
makeOrgPackageFromGAF() error with gene ID "GID"
AnnotationHub AnnotationDbi AnnotationForge
4 months ago Anna • 0
1
vote
5
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888
views
EnsDb: bad_weak_ptr
AnnotationHub BiocFileCache
5 months ago Lluís Revilla Sancho ▴ 760
0
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5
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1.1k
views
Cannot connect to annotationhub server
AnnotationHub ExperimentHub
updated 5 months ago by 4.1k • written 5 months ago by • 0
0
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0
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288
views
News: AnnotationHub and ExperimentHub Access Downtime
AnnotationHub ExperimentHub
5 months ago shepherl 4.1k
1
vote
1
reply
373
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub ExperimentHub
updated 6 months ago by 67k • written 6 months ago by • 0
6
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12
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7.0k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
13 months ago • updated 7 months ago shepherl 4.1k
10
votes
41
replies
7.3k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 6 months ago by • 0 • written 6.1 years ago by ★ 4.1k
1
vote
6
replies
958
views
unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 8 months ago by ▴ 200 • written 8 months ago by • 0
2
votes
1
reply
715
views
clusterProfiler, AnnotationHub, and discrepancies in GO Terms
Atlanticsalmon clusterPro Salmosalar AnnotationHub GeneOntology
updated 9 months ago by 43k • written 9 months ago by • 0
0
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0
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424
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Annotatr Duplicate Entries
annotatr AnnotationHub
10 months ago hayleyw • 0
2
votes
28
replies
5.5k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 12 months ago by 67k • written 2.0 years ago by ▴ 10
3
votes
4
replies
1.9k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
1
vote
2
replies
974
views
AnnotationHub data for Mus musculus seems to be missing, while previously it was there
tximeta AnnotationHub AnnotationHubData
14 months ago Thon • 0
0
votes
1
reply
901
views
multiGSEA package in R not appropriately assigning metabolites to pathways?
metaboliteIDmapping AnnotationHub multiGSEA
23 months ago • updated 22 months ago Thomas • 0
2
votes
2
replies
996
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
2.3 years ago Lenny186 • 0
0
votes
3
replies
1.8k
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub org.Hs.eg.db ensembldb
2.4 years ago • updated 2.3 years ago sandmann.t ▴ 70
9
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21
replies
15k
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 2.4 years ago by ▴ 10 • written 4.1 years ago by ▴ 40
0
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2
replies
2.2k
views
AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub Install
updated 2.7 years ago by 4.1k • written 2.7 years ago by ▴ 70
0
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4
replies
1.5k
views
AnnotationHub
AnnotationHub
2.7 years ago junliqilinpan • 0
4
votes
6
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3.0k
views
OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)
AnnotationHub OrganismDbi org.Hs.eg.db
updated 2.8 years ago by 52k • written 2.8 years ago by • 0
9
votes
14
replies
7.7k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 4 months ago by 4.1k • written 2.9 years ago by ▴ 40
0
votes
2
replies
1.3k
views
AnnotationHub problem
AnnotationHub
2.9 years ago Jianxuan • 0
4
votes
8
replies
2.3k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
3.0 years ago • updated 2.6 years ago nattzy94 ▴ 20
1
vote
3
replies
1.5k
views
How delete the AnnotationHub downloaded datasets
AnnotationHub
updated 3.1 years ago by ★ 6.6k • written 3.2 years ago by • 0
2
votes
10
replies
2.9k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 3.1 years ago by ★ 4.1k • written 3.2 years ago by • 0
0
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0
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732
views
LRBaseDbi error
LRBaseDbi AnnotationHub
3.3 years ago Francois Marchildon ▴ 20
1
vote
2
replies
1.8k
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb Bioconductor AnnotationHub clusterProfiler
updated 3.6 years ago by ★ 4.1k • written 3.6 years ago by • 0
0
votes
1
reply
1.3k
views
News: Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache AnnotationHub ExperimentHub cache
3.7 years ago shepherl 4.1k
0
votes
3
replies
5.2k
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub biomaRt
updated 2.3 years ago by • 0 • written 3.7 years ago by ▴ 20
3
votes
11
replies
6.1k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 10 months ago by ★ 4.1k • written 3.9 years ago by • 0
11
votes
13
replies
5.1k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
4.0 years ago • updated 3.9 years ago rohitsatyam102 ▴ 20
3
votes
2
replies
2.4k
views
Issue with AnnotationHub
AnnotationHub
4.0 years ago rahnaman ▴ 10
1
vote
2
replies
1.4k
views
How to mimic biomaRt results with AnnotationHub?
biomaRt AnnotationHub
4.1 years ago Ezgi ▴ 60
1
vote
3
replies
1.3k
views
AnnotationHub: failed to load resource name
AnnotationHub
4.3 years ago ben.ponv • 0
4
votes
17
replies
3.0k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by ▴ 10
4
votes
2
replies
2.0k
views
News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
4.3 years ago Johannes Rainer ★ 2.1k
8
votes
16
replies
8.0k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 4.4 years ago by 4.1k • written 4.4 years ago by ▴ 660
0
votes
2
replies
1.6k
views
Can't select GO from AnnotationHub orgDB packages
GO.db AnnotationHub OrgDB
updated 4.4 years ago by 67k • written 4.4 years ago by ★ 2.0k
0
votes
3
replies
1.3k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 4.5 years ago by 67k • written 4.5 years ago by ▴ 670
3
votes
6
replies
2.8k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 2.4 years ago by 4.1k • written 4.6 years ago by ★ 2.0k
2
votes
8
replies
2.1k
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error enrichGO annotationHub clusterProfiler Job
updated 4.6 years ago by 67k • written 4.6 years ago by • 0
1
vote
5
replies
2.0k
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 4.7 years ago by 4.1k • written 4.7 years ago by • 0
0
votes
2
replies
1.2k
views
hg38 tracks for AnnotationHub
annotationhub
4.8 years ago Michael Love 43k
0
votes
1
reply
1.1k
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 4.8 years ago by 4.1k • written 4.8 years ago by • 0
0
votes
8
replies
3.3k
views
I can't use AnnotationHub()
AnnotationHub
4.9 years ago 755606975 • 0
1
vote
3
replies
2.6k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub Ensembl Mouse AnnotationHub Ensembl
5.0 years ago dmgatti ▴ 10
3
votes
0
replies
1.4k
views
News: EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation ensembldb EnsDb AnnotationHub News
5.0 years ago Johannes Rainer ★ 2.1k
2
votes
2
replies
1.5k
views
how to choose annotation file in AnnotationHub web server
annotation AnnotationHub
5.1 years ago 15958021290 ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: Deseq2 Design by James W. MacDonald 67k
Trying to use a conventional factor analysis, particularly if you are new, is not the way to go (I have been doing this for over 20 years n…
Answer: p value is 0, padj is 0 by swbarnes2 ★ 1.4k
I think the default smallest value R will return is 1x10^-300. So I'd take a look at the counts, and see if it makes sense that the p-valu…
Comment: p value is 0, padj is 0 by Michael Love 43k
``` > set.seed(1); t.test(rnorm(200,rep(c(0,80),each=100)) ~ rep(0:1,each=100))$p.value [1] 0 ```
Answer: Cannot install GO.db and org.Hs.eg.db by James W. MacDonald 67k
You might try tracing the namespace loading. ``` Sys.setenv("_R_TRACE_LOADNAMESPACE_"="2") install("org.Hs.eg.db") ``` And see if th…
Answer: p value is 0, padj is 0 by James W. MacDonald 67k
It is quite possible for a very small p-value to remain very small after multiplicity adjustment. I don't know the cutoff for `DESeq2` to r…
Votes
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
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