Showing : ensembldb • reset
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 4 weeks ago by • 0 • written 5.5 years ago by ★ 3.9k
10
votes
18
replies
2.9k
views
ensembldb support for Ensembl's transcript_name column
ensembldb
updated 2.5 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 6.1 years ago by ★ 2.0k • written 6.1 years ago by ▴ 100
2
votes
12
replies
1.7k
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
5.8k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 7 weeks ago by 3.9k • 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
6.3 years ago • updated 6.2 years ago floriandeckert ▴ 30
6
votes
10
replies
2.3k
views
ensembldb: ensDbFromGtf error with ensembl version 74
ensembldb
updated 8.0 years ago by ★ 2.0k • written 8.0 years ago by ▴ 90
0
votes
10
replies
843
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 5.5 years ago by ▴ 20
3
votes
8
replies
4.4k
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 6.7 years ago by ★ 2.0k • written 6.7 years ago by ▴ 40
5
votes
6
replies
3.4k
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 4.6 years ago by ★ 3.3k • written 4.6 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 21 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
800
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
6 months ago • updated 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 19 months ago by ★ 3.9k • written 19 months ago by ▴ 30
0
votes
5
replies
2.0k
views
error when using ensembldb with a MySQL server
ensembldb rmysql
updated 6.4 years ago by 65k • written 6.4 years ago by ▴ 10
2
votes
5
replies
264
views
get BM error
ensembldb
updated 11 days ago by 65k • written 12 days ago by • 0
0
votes
4
replies
562
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 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
739
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
1.0k
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 2.4 years ago by ★ 2.0k • written 2.4 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
315
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
12 weeks ago Kai Hu ▴ 70
0
votes
3
replies
1.8k
views
errors with makeTxDbFromBiomart
biomart genomicfeatures maketxdbfrombiomart ensembldb ensDbFromGtf
updated 6.8 years ago by ★ 2.0k • written 6.8 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 16 months ago jamie.gearing ▴ 60
2
votes
3
replies
2.3k
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
837
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 2.6 years ago by ★ 6.5k • written 2.6 years ago by • 0
2
votes
3
replies
503
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio cDNA ensembldb NCBI
5 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 6.0 years ago by ★ 2.0k • written 6.0 years ago by ▴ 30
0
votes
3
replies
2.3k
views
incorrect biomaRt output order of gene list
biomart ensembldb error
6.2 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
988
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
1.1k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt ensembldb RNA ensembl
updated 13 months ago by ★ 2.0k • written 13 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
2.2 years ago Matthew Thornton ▴ 350
50 results • Page 1 of 1
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Comment: Couldn't connect to server while using "pathways" by ATpoint ★ 4.1k
Please understand that we neither can see your screen, nor read minds. You at least need to provide the line of code and the name of the pa…
Answer: Method to find pathways different between 2 groups by Gordon Smyth 50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of unavailability.…
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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