Showing : ensembldb • reset
2
votes
0
replies
74
views
News: News:Ensembl 106 has just been released!
ensembl biomaRt ensembldb
4 weeks ago Benjamin ▴ 20
2
votes
2
replies
140
views
ensembldb to make the EnsDb for Human Version 105 using 'fetchTablesFromEnsembl' I'm on day two, can it be sped up?
ensembldb
10 weeks ago Matthew Thornton ▴ 350
0
votes
1
reply
178
views
How to get the rsID of 4 million SNPA
ensembldb SNP SNPData genomes
updated 11 weeks ago by 3.5k • written 11 weeks ago by • 0
8
votes
9
replies
703
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 3 months ago by 15k • written 3 months ago by ▴ 30
0
votes
2
replies
313
views
Can't convert dog ensembl IDs into gene names
biomaRt ensembldb
updated 4 months ago by ★ 1.2k • written 4 months ago by • 0
0
votes
3
replies
368
views
Error: package or namespace load failed for 'EnsDb.Mmusculus.v79'
EnsDb.Mmusculus.v79 EnsDb.Mmusculus.v75 ensembldb
updated 4 months ago by ★ 1.9k • written 4 months ago by • 0
1
vote
0
replies
146
views
News: Ensembl 105 has just been released!
ensembl biomaRt ensembldb
5 months ago mchakiachvili ▴ 20
0
votes
0
replies
183
views
How to get Cytogenetic band for muscles gene by using Biomart or other tools in R
Annotation biomaRt ensembldb
5 months ago Liting • 0
10
votes
18
replies
994
views
ensembldb support for Ensembl's transcript_name column
ensembldb
updated 6 months ago by 15k • written 6 months ago by 36k
0
votes
3
replies
264
views
Problem select / ensembl package
ensembldb
6 months ago yinnahm • 0
2
votes
3
replies
398
views
biomart query in R is not matching ensembl website - missing results
ensembldb biomaRt
updated 7 months ago by ★ 5.5k • written 7 months ago by • 0
0
votes
3
replies
302
views
Error using old ensembldb annotations with R 4.0 +
anno EnsDb.Hsapiens.v79 ensDb.HSapiens.v92 AnnotationDbi ensembldb
9 months ago rbenel ▴ 20
1
vote
9
replies
520
views
How to filter EnsDb into another EnsDb object instead of GRange?
ens ensembldb EnsDb.Hsapiens.v86 EnsDb.Rnorvegicus.v75
11 months ago Ahdee ▴ 50
1
vote
0
replies
345
views
News: Ensembl 104 has just been released!
ensembldb biomaRt
12 months ago mchakiachvili ▴ 20
2
votes
1
reply
314
views
Retrieve gene description with ensembldb
biomaRt ensembldb AnnotationData
updated 13 months ago by ★ 1.9k • written 13 months ago by ▴ 480
1
vote
2
replies
342
views
Unable to use ensembldb's "ensDbFromGff()" function on .gff file from NCBI
ensembldb RNASeq
13 months ago Torkel • 0
0
votes
2
replies
520
views
News: Ensembl 103 has been released
biomaRt ensembldb Ensembl ensemblVEP Biomart
15 months ago • updated 12 months ago mchakiachvili ▴ 20
3
votes
2
replies
659
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi ensembldb
15 months ago Ezgi ▴ 30
0
votes
2
replies
833
views
mapping gene type or biotype to ENSEMBL ID
ensembldb biomaRt org.Hs.eg.db Annotation
updated 16 months ago by ★ 1.9k • written 16 months ago by • 0
1
vote
1
reply
375
views
topGO question
Ensembl ensembldb
updated 17 months ago by 59k • written 17 months ago by • 0
0
votes
0
replies
316
views
News: Ensembl 102 has been released
Ensembl biomaRt BioMar ensembldb
17 months ago mchakiachvili ▴ 20
0
votes
4
replies
408
views
Gene information (GRanges + sequence) to GenBank
granges genomic ranges genbankr ensembldb
updated 19 months ago by 59k • written 19 months ago by ▴ 20
4
votes
2
replies
527
views
News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
20 months ago Johannes Rainer ★ 1.9k
0
votes
1
reply
595
views
ensembldb package installation issue
ensembldb package installation BiocManager
updated 21 months ago by 3.5k • written 21 months ago by • 0
1
vote
1
reply
286
views
Is transcript color accessible through ensembldb? (gold = in both HAVANA+ENSEMBL)
ensembldb
updated 22 months ago by ★ 1.9k • written 22 months ago by ▴ 140
1
vote
0
replies
395
views
News: ensembldb EnsDb databases for Ensembl release 100 added to AnnotationHub
ensembl annotation ensembldb News
2.0 years ago Johannes Rainer ★ 1.9k
2
votes
1
reply
280
views
protein_domain_source from ensembldb and mapping with PFAM.db
ensembldb pfam.db
2.1 years ago bruce.moran ▴ 30
0
votes
1
reply
644
views
ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
2.1 years ago Assa Yeroslaviz ★ 1.5k
2
votes
12
replies
624
views
BioFileCache Problem and not linking to ensembldb problem in TxiMeta
Tximeta BioFileCache Ensembldb
updated 2.2 years ago by 25k • written 2.2 years ago by ▴ 20
3
votes
0
replies
390
views
News: EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation ensembldb EnsDb AnnotationHub News
2.5 years ago Johannes Rainer ★ 1.9k
5
votes
6
replies
1.5k
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 2.6 years ago by ★ 2.8k • written 2.6 years ago by ▴ 80
1
vote
0
replies
406
views
News: ensembldb EnsDb databases for Ensembl release 97 added to AnnotationHub
annotation ensembldb Ensembl News
2.9 years ago Johannes Rainer ★ 1.9k
1
vote
1
reply
841
views
Retrieve canonical transcript for each gene via ensembldb R package
annotation ensembldb
updated 3.3 years ago by ★ 1.9k • written 3.3 years ago by • 0
7
votes
8
replies
2.1k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport ensembldb EnsDB.hsapiens.v86
updated 3.4 years ago by 0 • written 3.5 years ago by ▴ 20
0
votes
1
reply
523
views
Pick coding vs non-coding from Ensembl data set
R ensembl ensembldb noncoding rna protein coding
updated 3.5 years ago by ★ 1.9k • written 3.5 years ago by • 0
5
votes
12
replies
1.3k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 2 hours ago by ★ 1.9k • written 3.5 years ago by ★ 3.2k
0
votes
5
replies
1.5k
views
mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus.v79
R annotation ensembldb
3.5 years ago foehn ▴ 80
1
vote
2
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1.4k
views
tximport using Ensembdb to create Tx2gene dataframe with bovine transcripts ?
tximport ensembldb bos taurus tx2gene
updated 3.8 years ago by 59k • written 3.8 years ago by • 0
0
votes
3
replies
2.0k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 4.0 years ago by ★ 1.9k • written 4.0 years ago by ▴ 30
6
votes
14
replies
1.5k
views
ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTablesFromEnsembl
ensembldb
updated 4.1 years ago by ★ 1.9k • written 4.1 years ago by ▴ 100
0
votes
3
replies
1.4k
views
incorrect biomaRt output order of gene list
biomart ensembldb error
4.2 years ago Yuqia • 0
2
votes
4
replies
6.4k
views
converting ensembl transcript ID to ensemble gene: problem & missing values
biomart error ensembldb
4.2 years ago Yuqia • 0
6
votes
11
replies
1.7k
views
ensembldb from M.musculus NCBI37 v67 gtf
ensembldb NCBI37 v67 ensembl
4.3 years ago floriandeckert ▴ 30
5
votes
9
replies
2.1k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
4.3 years ago emmak ▴ 20
1
vote
3
replies
947
views
how to get intron with ensembldb. package?
granges ensembldb GenomicFeatures
4.3 years ago alessandro.pastore ▴ 20
2
votes
2
replies
693
views
ensembldb and pseudogenes mapping to the same Ensembl ID
ensembldb
4.4 years ago meeta.mistry ▴ 20
0
votes
5
replies
1.3k
views
error when using ensembldb with a MySQL server
ensembldb rmysql
updated 4.4 years ago by 59k • written 4.4 years ago by ▴ 10
1
vote
0
replies
1.0k
views
News: Ensembl 91 EnsDb databases added to AnnotationHub
annotation ensembldb ensembl News
4.4 years ago Johannes Rainer ★ 1.9k
1
vote
2
replies
1.5k
views
Error : object path is not exported by namespace:Rsamtools
packages installation problem rsamtools chippeakanno ensembldb
4.4 years ago inzirio ▴ 10
1
vote
2
replies
780
views
get_gene_transcript_exon_tables.pl extremely slow
ensembl ensembldb
updated 4.5 years ago by ★ 1.9k • written 4.5 years ago by ▴ 230
50 results • Page 1 of 1
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Replies
Comment: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0 by Yang Shi • 0
Perfect answer! This questions troubled me for a long time. Thanks again and for your quick and detailed reply.
Comment: HTSeq Counts no longer available by swbarnes2 ★ 1.0k
STAR's output was intended to mimic HTseq-counts.
Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0 by James W. MacDonald 59k
In the previous post I noted that `paCalls` doesn't exist for this array, and that is still true today. And there are no methods similar to…
Comment: DiffBind GreyListChIP error: Error: BiocParallel errors by Rory Stark ★ 4.4k
Could you let me know the versions? Output of `sessionInfo()`.
Comment: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o by Yang Shi • 0
okay sir, the new post is here (https://support.bioconductor.org/p/9144266/). Looking forward to your reply.
Votes
Answer: Variance explained (coefficient of determination) in edgeR
HTSeq Counts no longer available
Comment: Problem converting transcript to genomic coordinates with Annotation Hub
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
C: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o
Awards • All
Popular Question to Johannes Rainer ★ 1.9k
Popular Question to Gordon Smyth 45k
Popular Question to Julie Zhu ★ 4.3k
Scholar to Hervé Pagès 15k
Commentator to James W. MacDonald 59k
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