Showing : Annotationhub • reset
9
votes
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 20 months ago by ▴ 10 • written 3.4 years ago by ▴ 40
7
votes
11
replies
6.4k
views
Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.probes
edgeR limma annotationhub kegga annotationdbi
updated 7.8 years ago by ▴ 20 • written 8.1 years ago by ▴ 20
8
votes
16
replies
6.1k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 3.7 years ago by 3.8k • written 3.7 years ago by ▴ 660
9
votes
11
replies
5.6k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 5 weeks ago by 3.8k • written 2.2 years ago by ▴ 40
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 13 days ago by • 0 • written 5.4 years ago by ★ 3.9k
7
votes
44
replies
5.4k
views
OrgDB download failed via AnnotationHub
annotationhub orgdb
updated 4.8 years ago by 3.8k • written 4.8 years ago by • 0
3
votes
11
replies
4.9k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 10 weeks ago by ★ 3.9k • written 3.2 years ago by • 0
0
votes
14
replies
4.8k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
7.2 years ago • updated 20 months ago Jenny Drnevich ★ 2.0k
6
votes
9
replies
4.5k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
updated 5 weeks ago by • 0 • written 5 months ago by 3.8k
8
votes
4
replies
4.4k
views
Tutorial: Epigenomics RoadMap Project files now accessible via AnnotationHub
AnnotationHub Epigenomics BigData RoadMap Project NIH Tutorial
updated 7.0 years ago by • 0 • written 8.9 years ago by ▴ 390
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
0
votes
3
replies
4.1k
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
9
replies
4.0k
views
AnnotationHub corrupt database
annotationhub
updated 5.1 years ago by 3.8k • written 8.7 years ago by ▴ 180
11
votes
13
replies
3.9k
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
4
votes
1
reply
3.7k
views
getting the longest transcript by gene from Refseq
refseq annotationhub
updated 8.6 years ago by 25k • written 8.6 years ago by ▴ 50
1
vote
6
replies
3.5k
views
failed to load 'AnnotationHub' resource
annotationhub annotation error
8.3 years ago elhananby ▴ 10
1
vote
3
replies
3.5k
views
Problem using display() function on RStudio
display rstudio annotationhub
updated 8.6 years ago by 65k • written 8.6 years ago by ▴ 10
2
votes
0
replies
3.3k
views
News: Gencode GFF3 and FASTA files now available via AnnotationHub
AnnotationHub Gencode GFF3 FASTA News
8.6 years ago Sonali Arora ▴ 390
2
votes
12
replies
3.1k
views
Error: failed to load 'AnnotationHub' resource
biomart annotationhub
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 10
0
votes
8
replies
2.7k
views
I can't use AnnotationHub()
AnnotationHub
4.3 years ago 755606975 • 0
0
votes
1
reply
2.6k
views
AnnotationHub - Problem with SSL CA certificate
annotationhub dependencies
8.3 years ago dalloliogm ▴ 50
3
votes
13
replies
2.6k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub organismdb orgdb unsupported organisms
updated 8.2 years ago by ★ 6.8k • written 8.2 years ago by ★ 3.9k
0
votes
8
replies
2.6k
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
8.6 years ago J.C. SUN • 0
5
votes
11
replies
2.5k
views
Certificate problem with ExperimentHub / AnnotationHub
software error curatedmetagenomicdata annotationhub experimenthub
updated 7.3 years ago by ★ 1.1k • written 7.3 years ago by ▴ 10
4
votes
17
replies
2.4k
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
2
votes
12
replies
2.3k
views
AnnotationHub-cant extract database
annotationhub
updated 7.0 years ago by ★ 6.8k • written 7.0 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
1
vote
6
replies
2.3k
views
Problem with AnnotationHub()
annotationhub
updated 7.3 years ago by ★ 6.8k • written 7.3 years ago by ▴ 10
1
vote
3
replies
2.2k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub Ensembl Mouse AnnotationHub Ensembl
4.3 years ago dmgatti ▴ 10
4
votes
6
replies
2.2k
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
0
votes
4
replies
2.2k
views
AnnotationHub Error HTTP status was '500 Internal Server Error'
annotationhub software error
8.3 years ago ness • 0
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
1
vote
3
replies
2.0k
views
annotation of SV (Structural Variants)
variantannotation annotationhub
7.1 years ago Bogdan ▴ 670
3
votes
2
replies
2.0k
views
Issue with AnnotationHub
AnnotationHub
3.4 years ago rahnaman ▴ 10
2
votes
2
replies
1.9k
views
Normal Patient Samples from GSE62944
GSE62944 annotationhub differentialexpression
updated 8.0 years ago by ▴ 390 • written 8.0 years ago by • 0
4
votes
3
replies
1.9k
views
Error installing AnnotationHub on Fedora
Annotationhub curl httr fedora
updated 7.9 years ago by ▴ 30 • written 8.6 years ago by ▴ 10
0
votes
1
reply
1.9k
views
Map siRNA-Sequence to Gene
sequence annotationhub biostrings
updated 8.7 years ago by 16k • written 8.7 years ago by • 0
0
votes
2
replies
1.8k
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
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
0
votes
5
replies
1.8k
views
Why are important organisms missing from AnnotationHub() $rdataclass == "OrgDb"?
annotationhub orgdb
updated 8.4 years ago by ★ 6.8k • written 8.4 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
3
replies
1.7k
views
annotationhub, download corrrupt,
annotationhub
8.5 years ago acaugu ▴ 10
2
votes
8
replies
1.7k
views
Problem fetching resources from AnnotationHub, error 403
AnnotationHub
updated 8.4 years ago by ★ 6.8k • written 8.5 years ago by ★ 2.0k
0
votes
2
replies
1.7k
views
Generating database with non model species to be use by ReportingTools
reportingtools annotationdbi annotationhub ensembldb
updated 7.8 years ago by ★ 2.0k • written 7.8 years ago by ▴ 20
1
vote
2
replies
1.6k
views
AnnotationHub: change download location of database
annotationhub installation
updated 8.4 years ago by 25k • written 8.4 years ago by ★ 3.9k
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
0
votes
1
reply
1.6k
views
Additions to AnnotationHub (for example, CpG islands for hg38 and mm10)
annotationhub
updated 7.4 years ago by ★ 6.8k • written 7.4 years ago by ▴ 140
4
votes
2
replies
1.6k
views
News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
3.6 years ago Johannes Rainer ★ 2.0k
3
votes
2
replies
1.6k
views
AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
annotationhub roadmap project rpkm data.frame
7.5 years ago wcstcyx ▴ 30
0
votes
2
replies
1.6k
views
bad restore file magic number with AnnotationHub
annotationhub
updated 7.4 years ago by ★ 6.8k • written 7.4 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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