Showing : AnnotationHub • reset
0
votes
6
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334
views
unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 24 days ago by ▴ 180 • written 4 weeks ago by • 0
2
votes
1
reply
334
views
clusterProfiler, AnnotationHub, and discrepancies in GO Terms
Atlanticsalmon clusterPro Salmosalar AnnotationHub GeneOntology
updated 9 weeks ago by 41k • written 9 weeks ago by • 0
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0
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168
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Annotatr Duplicate Entries
annotatr AnnotationHub
3 months ago hayleyw • 0
3
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4
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1.2k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 6 months ago by ★ 3.9k • written 6 months ago by • 0
6
votes
12
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4.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
6 months ago • updated 12 days ago shepherl 3.9k
1
vote
2
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574
views
AnnotationHub data for Mus musculus seems to be missing, while previously it was there
tximeta AnnotationHub AnnotationHubData
6 months ago Thon • 0
0
votes
1
reply
698
views
multiGSEA package in R not appropriately assigning metabolites to pathways?
metaboliteIDmapping AnnotationHub multiGSEA
15 months ago Thomas • 0
2
votes
28
replies
4.4k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 5 months ago by 65k • written 17 months ago by ▴ 10
2
votes
2
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768
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
20 months ago Lenny186 • 0
0
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3
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1.2k
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub org.Hs.eg.db ensembldb
21 months ago • updated 20 months ago sandmann.t ▴ 70
0
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2
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1.9k
views
AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub Install
updated 2.1 years ago by 3.9k • written 2.1 years ago by ▴ 30
0
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4
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1.2k
views
AnnotationHub
AnnotationHub
2.1 years ago junliqilinpan • 0
4
votes
6
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2.3k
views
OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)
AnnotationHub OrganismDbi org.Hs.eg.db
updated 2.2 years ago by 50k • written 2.2 years ago by • 0
9
votes
11
replies
5.8k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 7 weeks ago by 3.9k • written 2.3 years ago by ▴ 40
0
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2
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976
views
AnnotationHub problem
AnnotationHub
2.3 years ago Jianxuan • 0
4
votes
8
replies
1.9k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
2.4 years ago • updated 23 months ago nattzy94 ▴ 20
2
votes
10
replies
2.3k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 2.5 years ago by ★ 3.9k • written 2.5 years ago by • 0
1
vote
3
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1.2k
views
How delete the AnnotationHub downloaded datasets
AnnotationHub
updated 2.5 years ago by ★ 6.5k • written 2.6 years ago by • 0
0
votes
0
replies
604
views
LRBaseDbi error
LRBaseDbi AnnotationHub
2.7 years ago Francois Marchildon ▴ 20
1
vote
2
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1.4k
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb Bioconductor AnnotationHub clusterProfiler
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by • 0
0
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1
reply
1.1k
views
News: Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache AnnotationHub ExperimentHub cache
3.1 years ago shepherl 3.9k
0
votes
3
replies
4.2k
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub biomaRt
updated 20 months ago by • 0 • written 3.1 years ago by ▴ 20
3
votes
11
replies
5.0k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 12 weeks ago by ★ 3.9k • written 3.3 years ago by • 0
3
votes
2
replies
2.0k
views
Issue with AnnotationHub
AnnotationHub
3.4 years ago rahnaman ▴ 10
11
votes
13
replies
4.0k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
3.4 years ago • updated 3.3 years ago rohitsatyam102 ▴ 20
1
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2
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1.2k
views
How to mimic biomaRt results with AnnotationHub?
biomaRt AnnotationHub
3.5 years ago Ezgi ▴ 60
9
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21
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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 21 months ago by ▴ 10 • written 3.5 years ago by ▴ 40
4
votes
17
replies
2.5k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by ▴ 10
1
vote
3
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1.0k
views
AnnotationHub: failed to load resource name
AnnotationHub
3.7 years ago ben.ponv • 0
4
votes
2
replies
1.6k
views
News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
3.7 years ago Johannes Rainer ★ 2.0k
8
votes
16
replies
6.2k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 3.8 years ago by 3.9k • written 3.8 years ago by ▴ 660
0
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2
replies
1.3k
views
Can't select GO from AnnotationHub orgDB packages
GO.db AnnotationHub OrgDB
updated 3.8 years ago by 65k • written 3.8 years ago by ★ 2.0k
0
votes
3
replies
1.1k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 3.9 years ago by 65k • written 3.9 years ago by ▴ 670
3
votes
6
replies
2.2k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 21 months ago by 3.9k • written 4.0 years ago by ★ 2.0k
2
votes
8
replies
1.7k
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error enrichGO annotationHub clusterProfiler Job
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
1
vote
5
replies
1.6k
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 4.1 years ago by 3.9k • written 4.1 years ago by • 0
0
votes
2
replies
965
views
hg38 tracks for AnnotationHub
annotationhub
4.2 years ago Michael Love 41k
0
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1
reply
937
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 4.2 years ago by 3.9k • written 4.2 years ago by • 0
0
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8
replies
2.7k
views
I can't use AnnotationHub()
AnnotationHub
4.3 years ago 755606975 • 0
1
vote
3
replies
2.3k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub Ensembl Mouse AnnotationHub Ensembl
4.4 years ago dmgatti ▴ 10
3
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0
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1.0k
views
News: EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation ensembldb EnsDb AnnotationHub News
4.4 years ago Johannes Rainer ★ 2.0k
2
votes
2
replies
1.2k
views
how to choose annotation file in AnnotationHub web server
annotation AnnotationHub
4.5 years ago 15958021290 ▴ 10
3
votes
4
replies
1.1k
views
Are AH52264, AH66175, and AH70594 duplicates?
AnnotationHub
updated 4.5 years ago by 3.9k • written 4.5 years ago by ▴ 160
1
vote
3
replies
1.0k
views
Problem with AnnotationHub after crash during first download of metadata
AnnotationHub
updated 4.7 years ago by 3.9k • written 4.7 years ago by ▴ 10
7
votes
44
replies
5.4k
views
OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 4.8 years ago by 3.9k • written 4.9 years ago by • 0
1
vote
4
replies
1.2k
views
AnnotationHub Server denied you to change the given directory
annotation annotationhub
updated 5.0 years ago by 3.9k • written 5.0 years ago by ▴ 10
0
votes
11
replies
1.8k
views
AH134 and other AnnotationHub objects unavailable as "defunct"
AnnotationHub
updated 5.0 years ago by 3.9k • written 5.0 years ago by ▴ 40
2
votes
0
replies
985
views
News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 5.0 years ago by • 0 • written 5.0 years ago by 3.9k
1
vote
1
reply
1.1k
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
5.1 years ago wecai • 0
0
votes
0
replies
980
views
News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
5.2 years ago shepherl 3.9k
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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