Showing : AnnotationHub • reset
6
votes
22
replies
2.8k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 2 days ago by • 0 • written 4.5 years ago by ★ 3.6k
0
votes
1
reply
252
views
multiGSEA package in R not appropriately assigning metabolites to pathways?
metaboliteIDmapping AnnotationHub multiGSEA
4 months ago Thomas • 0
0
votes
11
replies
719
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 6 months ago by 63k • written 6 months ago by • 0
2
votes
2
replies
363
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19 rtracklayer AnnotationHub
9 months ago Lenny186 • 0
0
votes
3
replies
511
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub org.Hs.eg.db ensembldb
10 months ago • updated 9 months ago sandmann.t ▴ 70
9
votes
21
replies
13k
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 10 months ago by ▴ 10 • written 2.6 years ago by ▴ 40
0
votes
2
replies
1.2k
views
AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub Install
updated 14 months ago by 3.5k • written 14 months ago by • 0
0
votes
4
replies
605
views
AnnotationHub
AnnotationHub
14 months ago junliqilinpan • 0
4
votes
6
replies
1.1k
views
OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)
AnnotationHub OrganismDbi org.Hs.eg.db
updated 15 months ago by 47k • written 15 months ago by • 0
8
votes
9
replies
3.2k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 16 months ago by 16k • written 16 months ago by ▴ 40
0
votes
2
replies
547
views
AnnotationHub problem
AnnotationHub
17 months ago Jianxuan • 0
4
votes
8
replies
1.1k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
18 months ago • updated 12 months ago nattzy94 ▴ 20
1
vote
3
replies
728
views
How delete the AnnotationHub downloaded datasets
AnnotationHub
updated 19 months ago by ★ 6.0k • written 20 months ago by • 0
2
votes
10
replies
1.5k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 19 months ago by ★ 3.6k • written 19 months ago by • 0
0
votes
0
replies
360
views
LRBaseDbi error
LRBaseDbi AnnotationHub
21 months ago Francois Marchildon ▴ 20
1
vote
2
replies
844
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb Bioconductor AnnotationHub clusterProfiler
updated 2.1 years ago by ★ 3.6k • written 2.1 years ago by • 0
0
votes
1
reply
713
views
News: Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache AnnotationHub ExperimentHub cache
2.2 years ago shepherl 3.5k
0
votes
3
replies
2.8k
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub biomaRt
updated 9 months ago by • 0 • written 2.2 years ago by ▴ 20
3
votes
8
replies
3.1k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 14 months ago by ★ 3.6k • written 2.3 years ago by • 0
11
votes
13
replies
2.4k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
2.5 years ago • updated 2.4 years ago rohitsatyam102 ▴ 20
3
votes
2
replies
1.3k
views
Issue with AnnotationHub
AnnotationHub
2.5 years ago rahnaman ▴ 10
1
vote
2
replies
772
views
How to mimic biomaRt results with AnnotationHub?
biomaRt AnnotationHub
2.6 years ago Ezgi ▴ 30
1
vote
3
replies
584
views
AnnotationHub: failed to load resource name
AnnotationHub
2.8 years ago ben.ponv • 0
4
votes
17
replies
1.7k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 2.8 years ago by 3.8k • written 2.8 years ago by ▴ 10
4
votes
2
replies
1.0k
views
News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
2.8 years ago Johannes Rainer ★ 2.0k
8
votes
16
replies
3.1k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 2.8 years ago by 3.5k • written 2.8 years ago by ▴ 660
0
votes
2
replies
789
views
Can't select GO from AnnotationHub orgDB packages
GO.db AnnotationHub OrgDB
updated 2.9 years ago by 63k • written 2.9 years ago by ★ 2.0k
0
votes
3
replies
694
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 3.0 years ago by 63k • written 3.0 years ago by ▴ 660
3
votes
6
replies
1.3k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 10 months ago by 3.5k • written 3.1 years ago by ★ 2.0k
2
votes
8
replies
965
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error enrichGO annotationHub clusterProfiler Job
updated 3.1 years ago by 63k • written 3.1 years ago by • 0
1
vote
5
replies
932
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 3.2 years ago by 3.5k • written 3.2 years ago by • 0
0
votes
2
replies
605
views
hg38 tracks for AnnotationHub
annotationhub
3.3 years ago Michael Love 40k
0
votes
1
reply
547
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub Shiny Rstudio
updated 3.3 years ago by 3.5k • written 3.3 years ago by • 0
0
votes
8
replies
1.6k
views
I can't use AnnotationHub()
AnnotationHub
3.4 years ago 755606975 • 0
1
vote
3
replies
1.8k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub Ensembl Mouse AnnotationHub Ensembl
3.5 years ago dmgatti ▴ 10
3
votes
0
replies
712
views
News: EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation ensembldb EnsDb AnnotationHub News
3.5 years ago Johannes Rainer ★ 2.0k
2
votes
2
replies
870
views
how to choose annotation file in AnnotationHub web server
annotation AnnotationHub
3.6 years ago 15958021290 ▴ 10
3
votes
4
replies
768
views
Are AH52264, AH66175, and AH70594 duplicates?
AnnotationHub
updated 3.6 years ago by 3.5k • written 3.6 years ago by ▴ 160
1
vote
3
replies
588
views
Problem with AnnotationHub after crash during first download of metadata
AnnotationHub
updated 3.8 years ago by 3.5k • written 3.8 years ago by ▴ 10
7
votes
44
replies
3.3k
views
OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 3.9 years ago by 3.5k • written 4.0 years ago by • 0
2
votes
0
replies
617
views
News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 4.1 years ago by • 0 • written 4.1 years ago by 3.5k
1
vote
4
replies
749
views
AnnotationHub Server denied you to change the given directory
annotation annotationhub
updated 4.1 years ago by 3.5k • written 4.1 years ago by ▴ 10
0
votes
11
replies
1.2k
views
AH134 and other AnnotationHub objects unavailable as "defunct"
AnnotationHub
updated 4.1 years ago by 3.5k • written 4.1 years ago by ▴ 40
1
vote
1
reply
753
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
4.1 years ago wecai • 0
3
votes
9
replies
3.3k
views
AnnotationHub corrupt database
annotationhub
updated 4.2 years ago by 3.5k • written 7.9 years ago by ▴ 180
0
votes
0
replies
697
views
News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
4.3 years ago shepherl 3.5k
1
vote
7
replies
783
views
News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
4.6 years ago shepherl 3.5k
0
votes
5
replies
835
views
annotationhub: data update
annotationhub
updated 4.8 years ago by 3.5k • written 4.8 years ago by 6.5k
0
votes
0
replies
689
views
News: ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit annotationdata News
4.9 years ago shepherl 3.5k
1
vote
2
replies
1.2k
views
AnnotationHub, force update snapshot date?
annotationhub
updated 4.9 years ago by 3.5k • written 4.9 years ago by ▴ 80
50 results • Page 1 of 1
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Answer: multiple filters in biomaRt by RuBBiT0 ▴ 10
First, yes, one gene could be related to several GO ID, and the result is based on the annotation package you use. Second, could you pro…
Comment: Diffbind "No genome detected" by kyliecode • 0
Hi Dr. Stark, Thanks very much for your reply! The bam files were output from nf-core/chipseq pipeline and for some reason, they do not ha…
Answer: Discrepancy between DESeq2 files produced in Galaxy and R(RStudio) by Michael Love 40k
I guess that Galaxy may be using some kind of LFC shrinkage, but without seeing their code I wouldn't know for sure. Shrinkage generally…
Comment: TCGAbiolinks cannot find bcr_patient_barcode by Habil Zare ▴ 170
I checked your example with the devel version 2.29.6 on Bioc and it worked fine. Thanks for the fix!
Answer: error in ChAMP loading file by jenniferbrowngates • 0
I got a lot of information from this website about different topics which is beneficial for me too so I thank this site and also suggest a …
Votes
Answer: Using PEER to identify hidden confounders in RNA-seq data (not working)
Comment: Error: biomaRt has encountered an unexpected server error.
Comment: Interpret plot from DiffBind
Comment: Interpret plot from DiffBind
Comment: Interpret plot from DiffBind
Awards • All
Scholar to Tiago C. Silva ▴ 270
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Scholar to Rory Stark ★ 4.9k
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