Showing : ensembldb • reset
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
10
votes
18
replies
2.8k
views
ensembldb support for Ensembl's transcript_name column
ensembldb
updated 2.4 years ago by 16k • written 2.5 years ago by 41k
6
votes
14
replies
2.9k
views
ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTablesFromEnsembl
ensembldb
updated 6.0 years ago by ★ 2.0k • written 6.0 years ago by ▴ 100
2
votes
12
replies
1.6k
views
BioFileCache Problem and not linking to ensembldb problem in TxiMeta
Tximeta BioFileCache Ensembldb
updated 4.2 years ago by 25k • written 4.2 years ago by ▴ 30
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
6
votes
11
replies
3.2k
views
ensembldb from M.musculus NCBI37 v67 gtf
ensembldb NCBI37 v67 ensembl
6.2 years ago floriandeckert ▴ 30
6
votes
10
replies
2.2k
views
ensembldb: ensDbFromGtf error with ensembl version 74
ensembldb
updated 7.9 years ago by ★ 2.0k • written 7.9 years ago by ▴ 90
0
votes
10
replies
819
views
ensembldb::getGenomeTwoBitFile() not working for many species
AnnotationHubSoftware ensembldb
updated 7 months ago by 65k • written 7 months ago by • 0
5
votes
9
replies
3.5k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
6.2 years ago emmak ▴ 20
2
votes
9
replies
2.4k
views
ensembldb salmon deseq2 txt2import right tool?
ensembldb deseq2
6.9 years ago aaron.dickey • 0
4
votes
9
replies
2.1k
views
keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
ensdb.hsapiens.v75 ensembldb keys
updated 7.0 years ago by ★ 2.0k • written 7.0 years ago by ▴ 660
1
vote
9
replies
1.9k
views
How to filter EnsDb into another EnsDb object instead of GRange?
ens ensembldb EnsDb.Hsapiens.v86 EnsDb.Rnorvegicus.v75
2.9 years ago Ahdee ▴ 50
7
votes
8
replies
3.7k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport ensembldb EnsDB.hsapiens.v86
updated 5.3 years ago by 0 • written 5.4 years ago by ▴ 20
3
votes
8
replies
4.3k
views
EnsemblDb: how to retrieve gene name / description?
EnsDb.Mmusculus.v79 ensembldb annotation
updated 6.7 years ago by ★ 2.0k • written 6.7 years ago by ★ 3.9k
3
votes
7
replies
3.1k
views
ensDbFromGtf error from gtf file downloaded from GENCODE.
ensembldb ensdbfromgtf
updated 6.6 years ago by ★ 2.0k • written 6.6 years ago by ▴ 40
5
votes
6
replies
3.3k
views
How to build and map to a "pre-mRNA" reference transcriptome for single nucleus RNA-seq data?
tximeta ensembldb single-cell snRNA-seq tximport
updated 4.5 years ago by ★ 3.3k • written 4.5 years ago by ▴ 80
5
votes
6
replies
2.5k
views
Is mapId supposed to concatenate multiVals?
annotationdbi ensembldb
updated 6.9 years ago by ★ 2.0k • written 7.0 years ago by ★ 13k
7
votes
6
replies
4.1k
views
Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 6 months ago by 690 • written 20 months ago by ▴ 20
0
votes
5
replies
2.8k
views
mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus.v79
R annotation ensembldb
5.5 years ago foehn ▴ 100
2
votes
5
replies
763
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
5 months ago j_denton • 0
0
votes
5
replies
2.0k
views
Error when annotating ENSEMBLE transcript IDs from chicken annotation DB
R ensembldb Annotation
updated 18 months ago by ★ 3.9k • written 18 months ago by ▴ 30
0
votes
5
replies
1.9k
views
error when using ensembldb with a MySQL server
ensembldb rmysql
updated 6.3 years ago by 65k • written 6.3 years ago by ▴ 10
2
votes
5
replies
147
views
get BM error
ensembldb
updated 1 day ago by 65k • written 1 day ago by • 0
0
votes
4
replies
542
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
6 months ago Rockbar • 0
3
votes
4
replies
13k
views
converting ensembl transcript ID to ensemble gene: problem & missing values
biomart error ensembldb
6.2 years ago • updated 6.1 years ago Yuqia • 0
4
votes
4
replies
2.6k
views
Retrieve canonical transcript for each gene via ensembldb R package
annotation ensembldb
updated 21 months ago by ▴ 40 • written 5.3 years ago by • 0
2
votes
4
replies
721
views
Successor of genesBy Defunct Function
ensembldb
updated 15 months ago by 16k • written 15 months ago by ★ 1.5k
0
votes
4
replies
1.2k
views
Gene information (GRanges + sequence) to GenBank
granges genomic ranges genbankr ensembldb
updated 3.5 years ago by 65k • written 3.5 years ago by ▴ 20
0
votes
4
replies
1.1k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
19 months ago dario.beraldi • 0
2
votes
3
replies
1.7k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 15 months ago by • 0 • written 17 months ago by ▴ 10
0
votes
3
replies
998
views
Error using old ensembldb annotations with R 4.0 +
anno EnsDb.Hsapiens.v79 ensDb.HSapiens.v92 AnnotationDbi ensembldb
2.7 years ago rbenel ▴ 40
0
votes
3
replies
1.3k
views
Error: package or namespace load failed for 'EnsDb.Mmusculus.v79'
EnsDb.Mmusculus.v79 EnsDb.Mmusculus.v75 ensembldb
updated 2.3 years ago by ★ 2.0k • written 2.3 years ago by • 0
0
votes
3
replies
2.9k
views
Can't Install ensembldb and EnsDb.Hsapiens.v86
installation EnsDb.Hsapiens.v86 Bioconductor package ensembldb
22 months ago elmfinds • 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
2
votes
3
replies
295
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
11 weeks ago Kai Hu ▴ 70
0
votes
3
replies
1.8k
views
errors with makeTxDbFromBiomart
biomart genomicfeatures maketxdbfrombiomart ensembldb ensDbFromGtf
updated 6.7 years ago by ★ 2.0k • written 6.7 years ago by • 0
0
votes
3
replies
1.1k
views
Problem select / ensembl package
ensembldb
2.5 years ago yinnahm • 0
5
votes
3
replies
1.4k
views
Problem obtaining NCBI gene IDs from Ensembl version 107
biomaRt ensembldb ensembl
18 months ago • updated 15 months ago jamie.gearing ▴ 60
2
votes
3
replies
2.2k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 19 months ago by ▴ 120 • written 19 months ago by ▴ 10
1
vote
3
replies
815
views
Convert Chromosome postion to gene symbol
biomaRt ensembldb
16 months ago mbansal • 0
2
votes
3
replies
1.7k
views
biomart query in R is not matching ensembl website - missing results
ensembldb biomaRt
updated 2.5 years ago by ★ 6.5k • written 2.5 years ago by • 0
2
votes
3
replies
484
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio cDNA ensembldb NCBI
4 months ago R_Page • 0
5
votes
3
replies
1.7k
views
Is it possible to get Ensembl gene descriptions with ensembldb?
ensembldb
updated 6.9 years ago by ★ 2.0k • written 6.9 years ago by ▴ 90
0
votes
3
replies
4.3k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 5.9 years ago by ★ 2.0k • written 5.9 years ago by ▴ 30
0
votes
3
replies
2.3k
views
incorrect biomaRt output order of gene list
biomart ensembldb error
6.1 years ago Yuqia • 0
1
vote
3
replies
1.4k
views
how to get intron with ensembldb. package?
granges ensembldb GenomicFeatures
6.3 years ago alessandro.pastore ▴ 20
0
votes
3
replies
970
views
Uniprot IDs and NCBI taxonomy IDs to coding sequences
ensembldb biodbUniprot
updated 15 months ago by 65k • written 15 months ago by • 0
0
votes
2
replies
1.3k
views
News: Ensembl 103 has been released
biomaRt ensembldb Ensembl ensemblVEP Biomart
3.2 years ago • updated 3.0 years ago mchakiachvili ▴ 20
0
votes
2
replies
1.0k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt ensembldb RNA ensembl
updated 12 months ago by ★ 2.0k • written 12 months ago by • 0
2
votes
2
replies
1.1k
views
ensembldb to make the EnsDb for Human Version 105 using 'fetchTablesFromEnsembl' I'm on day two, can it be sped up?
ensembldb
2.1 years ago Matthew Thornton ▴ 350
50 results • Page 1 of 1
Recent ...
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
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…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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
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