Showing : annotationHub • reset
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
6 months ago • updated 3 days ago shepherl 3.8k
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 21 days ago by • 0 • written 5.4 years ago by ★ 3.9k
0
votes
6
replies
307
views
unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 14 days ago by ▴ 170 • written 23 days ago by • 0
2
votes
1
reply
323
views
clusterProfiler, AnnotationHub, and discrepancies in GO Terms
Atlanticsalmon clusterPro Salmosalar AnnotationHub GeneOntology
updated 7 weeks ago by 41k • written 8 weeks ago by • 0
0
votes
0
replies
155
views
Annotatr Duplicate Entries
annotatr AnnotationHub
3 months ago hayleyw • 0
2
votes
28
replies
4.3k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 4 months ago by 65k • written 16 months ago by ▴ 10
3
votes
4
replies
1.2k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 6 months ago by ★ 3.9k • written 6 months ago by • 0
1
vote
2
replies
551
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
687
views
multiGSEA package in R not appropriately assigning metabolites to pathways?
metaboliteIDmapping AnnotationHub multiGSEA
15 months ago • updated 14 months ago Thomas • 0
2
votes
2
replies
755
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
20 months ago • updated 19 months ago Lenny186 • 0
0
votes
3
replies
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
9
votes
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 21 months ago by ▴ 10 • written 3.5 years ago by ▴ 40
0
votes
2
replies
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 3.8k • written 2.1 years ago by ▴ 30
0
votes
4
replies
1.2k
views
AnnotationHub
AnnotationHub
2.1 years ago junliqilinpan • 0
4
votes
6
replies
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 2.1 years ago by 50k • written 2.1 years ago by • 0
9
votes
11
replies
5.7k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 6 weeks ago by 3.8k • written 2.3 years ago by ▴ 40
0
votes
2
replies
960
views
AnnotationHub problem
AnnotationHub
2.3 years ago Jianxuan • 0
4
votes
8
replies
1.8k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
2.4 years ago • updated 23 months ago nattzy94 ▴ 20
1
vote
3
replies
1.1k
views
How delete the AnnotationHub downloaded datasets
AnnotationHub
updated 2.5 years ago by ★ 6.5k • written 2.5 years ago by • 0
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
0
votes
0
replies
598
views
LRBaseDbi error
LRBaseDbi AnnotationHub
2.6 years ago Francois Marchildon ▴ 20
1
vote
2
replies
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
votes
1
reply
1.1k
views
News: Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache AnnotationHub ExperimentHub cache
3.1 years ago shepherl 3.8k
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
4.9k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 11 weeks ago by ★ 3.9k • written 3.2 years ago by • 0
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 3.2 years ago rohitsatyam102 ▴ 20
3
votes
2
replies
2.0k
views
Issue with AnnotationHub
AnnotationHub
3.4 years ago rahnaman ▴ 10
1
vote
2
replies
1.1k
views
How to mimic biomaRt results with AnnotationHub?
biomaRt AnnotationHub
3.5 years ago Ezgi ▴ 60
1
vote
3
replies
996
views
AnnotationHub: failed to load resource name
AnnotationHub
3.6 years ago ben.ponv • 0
4
votes
17
replies
2.5k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by ▴ 10
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 3.7 years ago by 3.8k • written 3.7 years ago by ▴ 660
0
votes
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 3.8k • written 3.9 years ago by ★ 2.0k
2
votes
8
replies
1.6k
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 3.8k • written 4.1 years ago by • 0
0
votes
2
replies
954
views
hg38 tracks for AnnotationHub
annotationhub
4.1 years ago Michael Love 41k
0
votes
1
reply
925
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 4.2 years ago by 3.8k • written 4.2 years ago by • 0
0
votes
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
votes
0
replies
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
4.4 years ago 15958021290 ▴ 10
3
votes
4
replies
1.1k
views
Are AH52264, AH66175, and AH70594 duplicates?
AnnotationHub
updated 4.5 years ago by 3.8k • 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 4.6 years ago by 3.8k • 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 3.8k • written 4.9 years ago by • 0
2
votes
0
replies
978
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 3.8k
1
vote
4
replies
1.2k
views
AnnotationHub Server denied you to change the given directory
annotation annotationhub
updated 5.0 years ago by 3.8k • 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 3.8k • written 5.0 years ago by ▴ 40
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
5.0 years ago wecai • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Hi, Yes, I've tried this, but I am not sure if it is possible to assign `bquote` values to the names of a vector. In particular, if I use…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Are you commenting on the OP's question, or adding a different question? If the latter, please start a new post rather than piggybacking on…
Answer: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Use `bquote`. See section 4.6 in [the vignette][1]. [1]: https://bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/in…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
I was thinking about removing unwanted variations at the sample level (ie a transformation shared across genes) not at the gene level. Corr…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
That's an assumption used for normalization of a sample, not an assumption you can use for an individual model. We always normalize to atte…
Votes
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Awards • All
Scholar to James W. MacDonald 65k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Locations • All
Canada, 5 minutes ago
France, 16 minutes ago
United States, 29 minutes ago
United States, 31 minutes ago
United States, 33 minutes ago
Traffic: 921 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6