Showing : AnnotationHub • reset
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News: AnnotationHub and ExperimentHub Access Downtime
AnnotationHub ExperimentHub
18 hours ago shepherl 3.9k
1
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1
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162
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Documenting resources in an `ExperimentHub` package?
AnnotationHub ExperimentHub
updated 27 days ago by 66k • written 28 days ago by • 0
6
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12
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5.5k
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BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
7 months ago • updated 8 weeks ago shepherl 3.9k
10
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41
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6.1k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 27 days ago by • 0 • written 5.6 years ago by ★ 4.0k
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6
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422
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unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 9 weeks ago by ▴ 180 • written 10 weeks ago by • 0
2
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1
reply
420
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clusterProfiler, AnnotationHub, and discrepancies in GO Terms
Atlanticsalmon clusterPro Salmosalar AnnotationHub GeneOntology
updated 3 months ago by 42k • written 3 months ago by • 0
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220
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Annotatr Duplicate Entries
annotatr AnnotationHub
4 months ago hayleyw • 0
2
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28
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4.6k
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Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 6 months ago by 66k • written 18 months ago by ▴ 10
3
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4
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1.3k
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Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
1
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2
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644
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AnnotationHub data for Mus musculus seems to be missing, while previously it was there
tximeta AnnotationHub AnnotationHubData
8 months ago Thon • 0
0
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1
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734
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multiGSEA package in R not appropriately assigning metabolites to pathways?
metaboliteIDmapping AnnotationHub multiGSEA
17 months ago • updated 16 months ago Thomas • 0
2
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2
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820
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[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
22 months ago • updated 21 months ago Lenny186 • 0
0
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3
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1.4k
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Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub org.Hs.eg.db ensembldb
22 months ago sandmann.t ▴ 70
9
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21
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15k
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ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tb…
AnnotationHub dplyr
updated 22 months ago by ▴ 10 • written 3.6 years ago by ▴ 40
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2
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1.9k
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AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub Install
updated 2.2 years ago by 3.9k • written 2.2 years ago by ▴ 50
0
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4
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1.2k
views
AnnotationHub
AnnotationHub
2.2 years ago junliqilinpan • 0
4
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6
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2.4k
views
OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)
AnnotationHub OrganismDbi org.Hs.eg.db
updated 2.3 years ago by 51k • written 2.3 years ago by • 0
9
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11
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6.2k
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Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 3 months ago by 3.9k • written 2.4 years ago by ▴ 40
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2
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1.0k
views
AnnotationHub problem
AnnotationHub
2.4 years ago Jianxuan • 0
4
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8
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2.0k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
2.5 years ago • updated 2.1 years ago nattzy94 ▴ 20
1
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3
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1.2k
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How delete the AnnotationHub downloaded datasets
AnnotationHub
updated 2.7 years ago by ★ 6.5k • written 2.7 years ago by • 0
2
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10
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2.4k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 2.7 years ago by ★ 4.0k • written 2.7 years ago by • 0
0
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0
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625
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LRBaseDbi error
LRBaseDbi AnnotationHub
2.8 years ago Francois Marchildon ▴ 20
1
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2
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1.5k
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb Bioconductor AnnotationHub clusterProfiler
updated 3.1 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
votes
1
reply
1.1k
views
News: Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache AnnotationHub ExperimentHub cache
3.2 years ago shepherl 3.9k
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3
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4.4k
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub biomaRt
updated 22 months ago by • 0 • written 3.2 years ago by ▴ 20
3
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11
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5.2k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 4 months ago by ★ 4.0k • written 3.4 years ago by • 0
11
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13
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4.3k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
3.6 years ago • updated 3.4 years ago rohitsatyam102 ▴ 20
3
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2
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2.1k
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Issue with AnnotationHub
AnnotationHub
3.5 years ago rahnaman ▴ 10
1
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2
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1.2k
views
How to mimic biomaRt results with AnnotationHub?
biomaRt AnnotationHub
3.6 years ago Ezgi ▴ 60
1
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3
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1.1k
views
AnnotationHub: failed to load resource name
AnnotationHub
3.8 years ago ben.ponv • 0
4
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17
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2.6k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 3.8 years ago by ★ 3.9k • written 3.8 years ago by ▴ 10
4
votes
2
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1.7k
views
News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
3.8 years ago Johannes Rainer ★ 2.1k
8
votes
16
replies
6.5k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 3.9 years ago by 3.9k • written 3.9 years ago by ▴ 660
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2
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1.4k
views
Can't select GO from AnnotationHub orgDB packages
GO.db AnnotationHub OrgDB
updated 3.9 years ago by 66k • written 3.9 years ago by ★ 2.0k
0
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3
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1.2k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 4.0 years ago by 66k • written 4.0 years ago by ▴ 670
3
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6
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2.4k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 23 months ago by 3.9k • written 4.1 years ago by ★ 2.0k
2
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8
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1.7k
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gene enrichment using enrichGO function throuth annotationHub orgDb
software error enrichGO annotationHub clusterProfiler Job
updated 4.1 years ago by 66k • written 4.1 years ago by • 0
1
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5
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1.7k
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 4.2 years ago by 3.9k • written 4.2 years ago by • 0
0
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2
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1.0k
views
hg38 tracks for AnnotationHub
annotationhub
4.3 years ago Michael Love 42k
0
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1
reply
968
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 4.3 years ago by 3.9k • written 4.3 years ago by • 0
0
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8
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2.8k
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I can't use AnnotationHub()
AnnotationHub
4.4 years ago 755606975 • 0
1
vote
3
replies
2.3k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub Ensembl Mouse AnnotationHub Ensembl
4.5 years ago dmgatti ▴ 10
3
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0
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1.1k
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News: EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation ensembldb EnsDb AnnotationHub News
4.6 years ago Johannes Rainer ★ 2.1k
2
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2
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1.3k
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how to choose annotation file in AnnotationHub web server
annotation AnnotationHub
4.6 years ago 15958021290 ▴ 10
3
votes
4
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1.2k
views
Are AH52264, AH66175, and AH70594 duplicates?
AnnotationHub
updated 4.7 years ago by 3.9k • written 4.7 years ago by ▴ 160
1
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3
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1.1k
views
Problem with AnnotationHub after crash during first download of metadata
AnnotationHub
updated 4.8 years ago by 3.9k • written 4.8 years ago by ▴ 10
7
votes
44
replies
5.7k
views
OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 4.9 years ago by 3.9k • written 5.0 years ago by • 0
2
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0
replies
1.0k
views
News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 5.1 years ago by • 0 • written 5.1 years ago by 3.9k
1
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4
replies
1.2k
views
AnnotationHub Server denied you to change the given directory
annotation annotationhub
updated 5.1 years ago by 3.9k • written 5.1 years ago by ▴ 10
50 results • Page 1 of 1
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Replies
Comment: Combining two bulk RNA seq datasets by Tanvi • 0
Thank you for your suggestion. However, my R version on server is 4.1.1 and BatchQC requires R version more than 4.3, but I created PCA plo…
Comment: Create multiple DoparParams with different number of registered cores by ATpoint ★ 4.2k
https://github.com/Bioconductor/BiocParallel/blob/devel/R/DoparParam-class.R DoparParam is a BiocParallel class, that is why I am asking …
Answer: Combining two bulk RNA seq datasets by W. Evan Johnson ▴ 850
Hello, I would recommend you use BatchQC (bioconductor package) to evaluate the extent to which batch effects impact your data. Not all bat…
Comment: Create multiple DoparParams with different number of registered cores by James W. MacDonald 66k
`registerDoParallel` and `DoparParam` are both `doParallel` functions, which again, is a CRAN package. What part of the code you present ab…
Answer: Create multiple DoparParams with different number of registered cores by Martin Morgan 25k
I think the answer is "you can't". `DoparParam()` provides a 'wrapper' around doParallel functionality, e.g., `bpworkers(DoparParam())` rea…
Votes
A: goana limma- extract list of DE genes and genes in the enriched GO terms?
A: goana limma- extract list of DE genes and genes in the enriched GO terms?
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
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