Showing : Annotationhub • reset
9
votes
21
replies
17k
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 3.4 years ago by ▴ 10 • written 5.1 years ago by ▴ 40
10
votes
41
replies
10k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 19 months ago by • 0 • written 7.1 years ago by ★ 4.1k
9
votes
14
replies
10k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 17 months ago by 4.2k • written 3.9 years ago by ▴ 40
8
votes
16
replies
9.6k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 5.4 years ago by 4.2k • written 5.4 years ago by ▴ 680
6
votes
12
replies
8.6k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
2.1 years ago • updated 20 months ago shepherl 4.2k
7
votes
44
replies
8.3k
views
OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 6.4 years ago by 4.2k • written 6.5 years ago by ▴ 10
3
votes
11
replies
7.7k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 22 months ago by ★ 4.1k • written 4.9 years ago by • 0
2
votes
28
replies
7.2k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
updated 2.0 years ago by 68k • written 3.0 years ago by ▴ 10
7
votes
11
replies
7.1k
views
Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.probes
edgeR limma annotationhub kegga annotationdbi
updated 9.4 years ago by ▴ 20 • written 9.8 years ago by ▴ 20
0
votes
3
replies
7.0k
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub biomaRt
updated 3.3 years ago by • 0 • written 4.7 years ago by ▴ 20
11
votes
13
replies
6.6k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
5.1 years ago • updated 4.9 years ago rohitsatyam102 ▴ 20
0
votes
14
replies
6.3k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
8.9 years ago • updated 3.3 years ago Jenny Drnevich ★ 2.0k
8
votes
4
replies
5.5k
views
Tutorial: Epigenomics RoadMap Project files now accessible via AnnotationHub
AnnotationHub Epigenomics BigData RoadMap Project NIH Tutorial
updated 8.6 years ago by • 0 • written 10.6 years ago by ▴ 390
3
votes
9
replies
4.9k
views
AnnotationHub corrupt database
annotationhub
updated 6.8 years ago by 4.2k • written 10.4 years ago by ▴ 180
1
vote
3
replies
4.5k
views
Problem using display() function on RStudio
display rstudio annotationhub
updated 10.3 years ago by 68k • written 10.3 years ago by ▴ 10
2
votes
0
replies
4.5k
views
News: Gencode GFF3 and FASTA files now available via AnnotationHub
AnnotationHub Gencode GFF3 FASTA News
10.3 years ago Sonali Arora ▴ 390
1
vote
6
replies
4.4k
views
failed to load 'AnnotationHub' resource
annotationhub annotation error
10.0 years ago elhananby ▴ 10
4
votes
1
reply
4.3k
views
getting the longest transcript by gene from Refseq
refseq annotationhub
updated 10.2 years ago by 25k • written 10.2 years ago by ▴ 50
2
votes
12
replies
4.2k
views
Error: failed to load 'AnnotationHub' resource
biomart annotationhub
updated 10.1 years ago by 25k • written 10.1 years ago by ▴ 10
4
votes
6
replies
4.1k
views
OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)
AnnotationHub OrganismDbi org.Hs.eg.db
updated 3.8 years ago by 53k • written 3.8 years ago by • 0
5
votes
11
replies
4.0k
views
Certificate problem with ExperimentHub / AnnotationHub
software error curatedmetagenomicdata annotationhub experimenthub
updated 9.0 years ago by ★ 1.1k • written 9.0 years ago by ▴ 10
0
votes
8
replies
3.9k
views
I can't use AnnotationHub()
AnnotationHub
5.9 years ago 755606975 • 0
4
votes
17
replies
3.9k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by ▴ 10
3
votes
13
replies
3.8k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub organismdb orgdb unsupported organisms
updated 9.9 years ago by ★ 6.8k • written 9.9 years ago by ★ 4.1k
2
votes
10
replies
3.6k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter annotationTools AnnotationHub AnnotationData
updated 4.2 years ago by ★ 4.1k • written 4.2 years ago by • 0
3
votes
6
replies
3.4k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub OrgDb snapshotDate
updated 3.4 years ago by 4.2k • written 5.6 years ago by ★ 2.0k
2
votes
12
replies
3.3k
views
AnnotationHub-cant extract database
annotationhub
updated 8.7 years ago by ★ 6.8k • written 8.7 years ago by • 0
0
votes
8
replies
3.1k
views
Usecase_AnnotationHub_GRanges.Rmd, genes = qhs[[1]] can't download UCSC 'refGene'. - Window 7, R 3.2.1, RStudio 0.99.484
annotationhub bioconductor for genomic data science
10.3 years ago J.C. SUN • 0
0
votes
1
reply
3.1k
views
AnnotationHub - Problem with SSL CA certificate
annotationhub dependencies
10.0 years ago dalloliogm ▴ 50
4
votes
8
replies
3.1k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
4.0 years ago • updated 3.6 years ago nattzy94 ▴ 20
1
vote
3
replies
3.1k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub Ensembl Mouse AnnotationHub Ensembl
6.0 years ago dmgatti ▴ 10
1
vote
6
replies
3.1k
views
Problem with AnnotationHub()
annotationhub
updated 9.0 years ago by ★ 6.8k • written 9.0 years ago by ▴ 10
3
votes
4
replies
2.9k
views
Annotation hub and clusterProfiler errors
clusterProfiler Annotationhub
updated 2.1 years ago by ★ 4.1k • written 2.1 years ago by • 0
2
votes
8
replies
2.9k
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error enrichGO annotationHub clusterProfiler Job
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
3
votes
2
replies
2.8k
views
Issue with AnnotationHub
AnnotationHub
5.0 years ago rahnaman ▴ 10
0
votes
11
replies
2.8k
views
AH134 and other AnnotationHub objects unavailable as "defunct"
AnnotationHub
updated 6.6 years ago by 4.2k • written 6.6 years ago by ▴ 40
0
votes
4
replies
2.7k
views
AnnotationHub Error HTTP status was '500 Internal Server Error'
annotationhub software error
9.9 years ago ness • 0
1
vote
2
replies
2.6k
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb Bioconductor AnnotationHub clusterProfiler
updated 4.6 years ago by ★ 4.1k • written 4.6 years ago by • 0
2
votes
2
replies
2.6k
views
Normal Patient Samples from GSE62944
GSE62944 annotationhub differentialexpression
updated 9.7 years ago by ▴ 390 • written 9.7 years ago by • 0
0
votes
3
replies
2.6k
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub org.Hs.eg.db ensembldb
3.4 years ago • updated 3.3 years ago sandmann.t ▴ 70
0
votes
2
replies
2.6k
views
bad restore file magic number with AnnotationHub
annotationhub
updated 9.0 years ago by ★ 6.8k • written 9.1 years ago by • 0
0
votes
2
replies
2.6k
views
AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub Install
updated 3.7 years ago by 4.2k • written 3.7 years ago by ▴ 70
1
vote
3
replies
2.6k
views
annotation of SV (Structural Variants)
variantannotation annotationhub
8.7 years ago Bogdan ▴ 670
0
votes
1
reply
2.5k
views
Map siRNA-Sequence to Gene
sequence annotationhub biostrings
updated 10.3 years ago by 16k • written 10.3 years ago by • 0
1
vote
5
replies
2.5k
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 5.7 years ago by 4.2k • written 5.7 years ago by • 0
0
votes
5
replies
2.5k
views
Why are important organisms missing from AnnotationHub() $rdataclass == "OrgDb"?
annotationhub orgdb
updated 10.1 years ago by ★ 6.8k • written 10.1 years ago by ▴ 10
5
votes
13
replies
2.5k
views
Installing annotation package in locally
AnnotationDbi AnnotationHub Annotation AnnotationForge
14 months ago • updated 13 months ago KABILAN • 0
0
votes
2
replies
2.4k
views
Generating database with non model species to be use by ReportingTools
reportingtools annotationdbi annotationhub ensembldb
updated 9.5 years ago by ★ 2.1k • written 9.5 years ago by ▴ 20
4
votes
2
replies
2.4k
views
News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
5.3 years ago Johannes Rainer ★ 2.1k
4
votes
7
replies
2.3k
views
AnnotationHub and ExperimentHub make "~" directory in my home
annotationhub experimenthub
updated 9.3 years ago by ★ 6.8k • written 9.3 years ago by 43k
131 results • Page 1 of 3
Recent ...
Replies
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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