Showing : Ensembldb • reset
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 15 days ago by • 0 • written 5.4 years ago by ★ 3.9k
0
votes
1
reply
146
views
Convert transcriptomic bam to genomic bam?
ensembldb transcriptome genome coordinateconversion
updated 18 days ago by 41k • written 20 days ago by ▴ 10
0
votes
1
reply
200
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
2
votes
3
replies
282
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
10 weeks ago Kai Hu ▴ 70
1
vote
1
reply
205
views
502 error biomaRt getLDS()
ensembldb biomaRt
updated 9 weeks ago by • 0 • written 10 weeks ago by ▴ 10
2
votes
3
replies
471
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
5
replies
736
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
4
replies
525
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
6 months ago • updated 5 months ago Rockbar • 0
0
votes
10
replies
812
views
ensembldb::getGenomeTwoBitFile() not working for many species
AnnotationHubSoftware ensembldb
updated 7 months ago by 65k • written 7 months ago by • 0
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
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
0
votes
1
reply
468
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 8 months ago by 65k • written 8 months ago by • 0
0
votes
1
reply
1.4k
views
News: News:Ensembl 110 has been released
ensembldb biomaRt
updated 9 months ago by 41k • written 9 months ago by ▴ 30
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
0
votes
0
replies
674
views
BiomaRt - Problem to access homolog lists
biomaRt ensembldb
14 months ago ginie.dub • 0
1
vote
0
replies
639
views
News: Ensembl 109 has been released
ensembldb
14 months ago Aleena ▴ 20
0
votes
3
replies
961
views
Uniprot IDs and NCBI taxonomy IDs to coding sequences
ensembldb biodbUniprot
updated 14 months ago by 65k • written 15 months ago by • 0
2
votes
4
replies
714
views
Successor of genesBy Defunct Function
ensembldb
updated 15 months ago by 16k • written 15 months ago by ★ 1.5k
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
1
vote
3
replies
801
views
Convert Chromosome postion to gene symbol
biomaRt ensembldb
16 months ago mbansal • 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
1
vote
2
replies
765
views
News: Ensembl 108 has been released!
biomaRt ensembldb ensembl
written 18 months ago by ▴ 10
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
4
replies
1.1k
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
3
replies
2.2k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 18 months ago by ▴ 120 • written 19 months ago by ▴ 10
0
votes
1
reply
705
views
getBM Error with certain attribute combinations
biomaRt ensembldb
updated 19 months ago by ★ 4.0k • written 19 months ago by • 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
20 months ago sandmann.t ▴ 70
1
vote
0
replies
788
views
News: Ensembl 107 has been released
ensembldb
21 months ago Aleena ▴ 20
0
votes
1
reply
1.0k
views
bioMart Sscrofa_gene_ensembl getBM() paralogues ERROR
biomaRt ensembldb paralogues
updated 21 months ago by ★ 1.6k • written 21 months ago by • 0
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
0
replies
706
views
News: News:Ensembl 106 has just been released!
ensembl biomaRt ensembldb
2.0 years ago Benjamin ▴ 30
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
0
votes
2
replies
2.5k
views
How to get the rsID of 4 million SNPA
ensembldb SNP SNPData genomes
written 2.2 years ago by • 0
9
votes
11
replies
5.7k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 5 weeks ago by 3.8k • written 2.2 years ago by ▴ 40
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
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
1
vote
0
replies
778
views
News: Ensembl 105 has just been released!
ensembl biomaRt ensembldb
2.4 years ago mchakiachvili ▴ 20
0
votes
1
reply
941
views
How to get Cytogenetic band for muscles gene by using Biomart or other tools in R
Annotation biomaRt ensembldb
written 2.4 years ago by • 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
0
votes
3
replies
1.1k
views
Problem select / ensembl package
ensembldb
2.5 years ago yinnahm • 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
0
votes
3
replies
992
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
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
1
vote
0
replies
990
views
News: Ensembl 104 has just been released!
ensembldb biomaRt
3.0 years ago mchakiachvili ▴ 20
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
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
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
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
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
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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