Showing : ensembldb • reset
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
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 2.2 years ago by ▴ 40
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 19 days ago by • 0 • written 5.4 years ago by ★ 3.9k
7
votes
6
replies
4.0k
views
Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 6 months ago by 690 • written 20 months ago by ▴ 20
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
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
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
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
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
5
votes
1
reply
3.3k
views
Tutorial: Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
shortread rsubread ensembldb Tutorial
8.0 years ago phil.chapman ▴ 150
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
5
votes
6
replies
2.5k
views
Is mapId supposed to concatenate multiVals?
annotationdbi ensembldb
updated 6.9 years ago by ★ 2.0k • written 6.9 years ago by ★ 13k
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
4
votes
9
replies
2.1k
views
keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
ensdb.hsapiens.v75 ensembldb keys
updated 6.9 years ago by ★ 2.0k • written 6.9 years ago by ▴ 660
4
votes
2
replies
1.6k
views
News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
3.7 years ago Johannes Rainer ★ 2.0k
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
3
votes
0
replies
1.0k
views
News: EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation ensembldb EnsDb AnnotationHub News
4.4 years ago Johannes Rainer ★ 2.0k
3
votes
2
replies
1.6k
views
tximport with versioned identifiers
tximport ensembldb
6.5 years ago Ed Siefker ▴ 230
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 ▴ 30
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
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
3
votes
1
reply
1.3k
views
Mouse to Human Genes using bioconductor
ensembldb
updated 8 months ago by 65k • written 8 months ago by ▴ 10
3
votes
2
replies
2.4k
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi ensembldb
3.2 years ago Ezgi ▴ 60
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
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
2
votes
3
replies
477
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
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
1
reply
1.4k
views
Retrieve gene description with ensembldb
biomaRt ensembldb AnnotationData
updated 3.0 years ago by ★ 2.0k • written 3.0 years ago by ▴ 490
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
2
votes
9
replies
2.4k
views
ensembldb salmon deseq2 txt2import right tool?
ensembldb deseq2
6.9 years ago aaron.dickey • 0
2
votes
3
replies
287
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
10 weeks ago Kai Hu ▴ 70
2
votes
4
replies
717
views
Successor of genesBy Defunct Function
ensembldb
updated 15 months ago by 16k • written 15 months ago by ★ 1.5k
2
votes
5
replies
751
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
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
2
votes
1
reply
842
views
protein_domain_source from ensembldb and mapping with PFAM.db
ensembldb pfam.db
4.0 years ago bruce.moran ▴ 30
2
votes
2
replies
2.6k
views
mapping gene type or biotype to ENSEMBL ID
ensembldb biomaRt org.Hs.eg.db Annotation
updated 3.3 years ago by ★ 2.0k • written 3.3 years ago by • 0
2
votes
0
replies
708
views
News: News:Ensembl 106 has just been released!
ensembl biomaRt ensembldb
2.0 years ago Benjamin ▴ 30
2
votes
2
replies
1.3k
views
ensembldb and pseudogenes mapping to the same Ensembl ID
ensembldb
6.3 years ago meeta.mistry ▴ 30
1
vote
0
replies
879
views
News: ensembldb EnsDb databases for Ensembl release 97 added to AnnotationHub
annotation ensembldb Ensembl News
4.8 years ago Johannes Rainer ★ 2.0k
1
vote
0
replies
640
views
News: Ensembl 109 has been released
ensembldb
14 months ago Aleena ▴ 20
1
vote
2
replies
13
views
get BM error
ensembldb
20 minutes ago • updated 3 minutes ago Fara • 0
1
vote
1
reply
1.3k
views
topGO question
Ensembl ensembldb
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
1
vote
0
replies
780
views
News: Ensembl 105 has just been released!
ensembl biomaRt ensembldb
2.4 years ago mchakiachvili ▴ 20
1
vote
0
replies
790
views
News: Ensembl 107 has been released
ensembldb
21 months ago Aleena ▴ 20
1
vote
2
replies
2.3k
views
tximport using Ensembdb to create Tx2gene dataframe with bovine transcripts ?
tximport ensembldb bos taurus tx2gene
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
1
vote
2
replies
768
views
News: Ensembl 108 has been released!
biomaRt ensembldb ensembl
written 18 months ago by ▴ 10
1
vote
2
replies
1.2k
views
get_gene_transcript_exon_tables.pl extremely slow
ensembl ensembldb
updated 6.5 years ago by ★ 2.0k • written 6.5 years ago by ▴ 230
1
vote
2
replies
2.4k
views
Error : object path is not exported by namespace:Rsamtools
packages installation problem rsamtools chippeakanno ensembldb
6.4 years ago inzirio ▴ 10
1
vote
2
replies
1.1k
views
Unable to use ensembldb's "ensDbFromGff()" function on .gff file from NCBI
ensembldb RNASeq
3.0 years ago Torkel • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: get BM error by Fara • 0
Thank you for the reply. The examples are these. ENSGACG00000014473 ENSGACG00000015168 ENSGACG00000007529
Comment: get BM error by Mike Smith ★ 6.5k
Can you provide an example of the Ensemble IDs you're trying to convert?
Comment: How to retrieve gene ontology GO class? by bandconductor • 0
Sorry I wasn't clear before. What I mean is the all the information associated with the go term, such as description and evidence. I have …
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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