Showing : Ensembldb • reset
6
votes
11
replies
3.2k
views
ensembldb from M.musculus NCBI37 v67 gtf
ensembldb NCBI37 v67 ensembl
6.2 years ago floriandeckert ▴ 30
7
votes
36
replies
5.4k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 11 days ago by • 0 • written 5.4 years ago by ★ 3.9k
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 ★ 3.2k • written 4.5 years ago by ▴ 80
5
votes
3
replies
1.7k
views
Is it possible to get Ensembl gene descriptions with ensembldb?
ensembldb
updated 6.8 years ago by ★ 2.0k • written 6.9 years ago by ▴ 90
9
votes
11
replies
5.6k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 4 weeks ago by 3.8k • written 2.2 years ago by ▴ 40
3
votes
4
replies
13k
views
converting ensembl transcript ID to ensemble gene: problem & missing values
biomart error ensembldb
6.1 years ago Yuqia • 0
0
votes
3
replies
2.2k
views
incorrect biomaRt output order of gene list
biomart ensembldb error
6.1 years ago Yuqia • 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
0
votes
3
replies
1.1k
views
Problem select / ensembl package
ensembldb
2.5 years ago yinnahm • 0
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
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
2
votes
2
replies
1.3k
views
ensembldb and pseudogenes mapping to the same Ensembl ID
ensembldb
6.3 years ago meeta.mistry ▴ 30
0
votes
3
replies
2.8k
views
Can't Install ensembldb and EnsDb.Hsapiens.v86
installation EnsDb.Hsapiens.v86 Bioconductor package ensembldb
21 months ago elmfinds • 0
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
278
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
9 weeks ago Kai Hu ▴ 70
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
4
votes
9
replies
2.0k
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
3
votes
2
replies
1.6k
views
tximport with versioned identifiers
tximport ensembldb
6.5 years ago Ed Siefker ▴ 230
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
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
5
votes
6
replies
2.4k
views
Is mapId supposed to concatenate multiVals?
annotationdbi ensembldb
updated 6.9 years ago by ★ 2.0k • written 6.9 years ago by ★ 13k
0
votes
1
reply
194
views
Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 9 weeks ago by 65k • written 9 weeks ago by ▴ 10
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
2
replies
1.1k
views
ENSEMBL_MART_FUNCGEN not accessible through biomaRt?
biomart regulatory ensemble mart ensembldb
updated 7.8 years ago by ▴ 800 • written 7.8 years ago by ▴ 50
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
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
3
votes
7
replies
3.0k
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
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
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
1
vote
3
replies
1.4k
views
how to get intron with ensembldb. package?
granges ensembldb GenomicFeatures
6.2 years ago alessandro.pastore ▴ 20
5
votes
9
replies
3.4k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
6.2 years ago emmak ▴ 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
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
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
0
votes
1
reply
976
views
Pick coding vs non-coding from Ensembl data set
R ensembl ensembldb noncoding rna protein coding
updated 5.4 years ago by ★ 2.0k • written 5.4 years ago by • 0
4
votes
4
replies
2.6k
views
Retrieve canonical transcript for each gene via ensembldb R package
annotation ensembldb
updated 20 months ago by ▴ 40 • written 5.2 years ago by • 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
834
views
protein_domain_source from ensembldb and mapping with PFAM.db
ensembldb pfam.db
4.0 years ago bruce.moran ▴ 30
1
vote
1
reply
759
views
Is transcript color accessible through ensembldb? (gold = in both HAVANA+ENSEMBL)
ensembldb
updated 3.8 years ago by ★ 2.0k • written 3.8 years ago by ▴ 160
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
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
2
votes
2
replies
2.5k
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
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
3
votes
1
reply
1.2k
views
Mouse to Human Genes using bioconductor
ensembldb
updated 8 months ago by 65k • written 8 months ago by ▴ 10
0
votes
2
replies
1.4k
views
Can't convert dog ensembl IDs into gene names
biomaRt ensembldb
updated 2.3 years ago by ★ 4.0k • written 2.3 years ago by • 0
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
0
votes
1
reply
1000
views
bioMart Sscrofa_gene_ensembl getBM() paralogues ERROR
biomaRt ensembldb paralogues
updated 21 months ago by ★ 1.6k • written 21 months ago by • 0
2
votes
1
reply
1.3k
views
Retrieve gene description with ensembldb
biomaRt ensembldb AnnotationData
updated 3.0 years ago by ★ 2.0k • written 3.0 years ago by ▴ 490
0
votes
4
replies
1.0k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
18 months ago dario.beraldi • 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 ...
Replies
Answer: Memory errors using read.bismark? by Peter Hickey ▴ 690
Thanks for sharing an example file. This is a very large non-CpG methylation dataset, which are tricky to work with for a number of reason…
Comment: Reading huge bismark coverage files using bbseq::read.bismark by Peter Hickey ▴ 690
Superficially, your issue is similar to [https://github.com/hansenlab/bsseq/issues/136](https://github.com/hansenlab/bsseq/issues/136). You…
Answer: Reading huge bismark coverage files using bbseq::read.bismark by Peter Hickey ▴ 690
I'm one of the **bsseq** developers. Are you able to share one of your files with me (e.g., via Dropbox, Google Drive, OneDrive, etc.). Tha…
Comment: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var by daniel.carbajo • 0
Yeah I think this is the way to go! How can I pass `col_list` here though? `Heatmap` does not accept a list of color vectors... How can I m…
Answer: The issue with SGSeq_analyzeFeatures() returns errors on BAM files by kamryncole1963 • 0
https://support.bioconductor.org/p/85837/[tunnel rush][1] Refer to this link, it may help. [1]: https://tunnelrush3.com
Votes
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
Comment: DESeq2 - Plot Nr. Genes vs Variance explained in PCA
Answer: How to retrieve detailed regression results from deseq2
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