Showing : ensembldb • reset
0
votes
4
replies
228
views
Biomart and ensembl not working?
ensembldb biomaRt
updated 5 days ago by 67k • written 5 days ago by • 0
0
votes
0
replies
272
views
News: Ensembl 113 has been released
ensembl ensembldb mart biomaRt
3 months ago Ensembl_Jorge • 0
1
vote
3
replies
1.1k
views
502 error biomaRt getLDS()
ensembldb biomaRt
updated 4 months ago by 67k • written 11 months ago by ▴ 10
0
votes
0
replies
337
views
Job: Ensembl Job Vacancies
genomes Annotation GenomicVariation ensembldb
4 months ago Aleena ▴ 30
1
vote
1
reply
580
views
biomaRt getSequence(): Error in .lock2
ensembldb getSequence
updated 5 months ago by ★ 6.6k • written 5 months ago by ▴ 10
1
vote
0
replies
496
views
News: Ensembl 112 has been released.
ensembldb biomaRt ensemblrelease
8 months ago Aleena ▴ 30
2
votes
5
replies
648
views
get BM error
ensembldb
updated 9 months ago by 67k • written 9 months ago by • 0
10
votes
41
replies
7.6k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 8 months ago by • 0 • written 6.2 years ago by ★ 4.1k
0
votes
1
reply
490
views
Convert transcriptomic bam to genomic bam?
ensembldb transcriptome genome coordinateconversion
updated 9 months ago by 43k • written 9 months ago by ▴ 10
0
votes
1
reply
620
views
Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 11 months ago by 67k • written 11 months ago by ▴ 10
2
votes
4
replies
1.1k
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
written 11 months ago by ▴ 70
2
votes
3
replies
790
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio cDNA ensembldb NCBI
13 months ago R_Page • 0
4
votes
6
replies
2.0k
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
updated 3 months ago by • 0 • written 14 months ago by • 0
0
votes
4
replies
1.0k
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
15 months ago Rockbar • 0
0
votes
10
replies
1.3k
views
ensembldb::getGenomeTwoBitFile() not working for many species
AnnotationHubSoftware ensembldb
updated 16 months ago by 67k • written 16 months ago by • 0
7
votes
6
replies
6.5k
views
Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 15 months ago by 700 • written 2.4 years ago by ▴ 20
3
votes
1
reply
3.7k
views
Mouse to Human Genes using bioconductor
ensembldb
updated 17 months ago by 67k • written 17 months ago by ▴ 10
0
votes
1
reply
768
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 17 months ago by 67k • written 17 months ago by • 0
0
votes
1
reply
2.5k
views
News: News:Ensembl 110 has been released
ensembldb biomaRt
updated 18 months ago by 43k • written 18 months ago by ▴ 30
0
votes
2
replies
1.6k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt ensembldb RNA ensembl
updated 21 months ago by ★ 2.1k • written 21 months ago by • 0
0
votes
0
replies
952
views
BiomaRt - Problem to access homolog lists
biomaRt ensembldb
23 months ago ginie.dub • 0
1
vote
0
replies
923
views
News: Ensembl 109 has been released
ensembldb
23 months ago Aleena ▴ 30
0
votes
3
replies
1.4k
views
Uniprot IDs and NCBI taxonomy IDs to coding sequences
ensembldb biodbUniprot
updated 24 months ago by 67k • written 24 months ago by • 0
2
votes
4
replies
1.0k
views
Successor of genesBy Defunct Function
ensembldb
updated 2.0 years ago by 16k • written 2.0 years ago by ★ 1.5k
5
votes
3
replies
2.1k
views
Problem obtaining NCBI gene IDs from Ensembl version 107
biomaRt ensembldb ensembl
2.2 years ago • updated 2.0 years ago jamie.gearing ▴ 60
1
vote
3
replies
1.3k
views
Convert Chromosome postion to gene symbol
biomaRt ensembldb
2.1 years ago mbansal • 0
2
votes
3
replies
2.4k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 24 months ago by • 0 • written 2.2 years ago by ▴ 10
1
vote
2
replies
1.0k
views
News: Ensembl 108 has been released!
biomaRt ensembldb ensembl
written 2.3 years ago by ▴ 10
0
votes
5
replies
2.8k
views
Error when annotating ENSEMBLE transcript IDs from chicken annotation DB
R ensembldb Annotation
updated 2.3 years ago by ★ 4.1k • written 2.3 years ago by ▴ 30
0
votes
4
replies
1.4k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
2.3 years ago dario.beraldi • 0
2
votes
3
replies
3.2k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 2.3 years ago by ▴ 140 • written 2.3 years ago by ▴ 10
0
votes
1
reply
898
views
getBM Error with certain attribute combinations
biomaRt ensembldb
updated 2.4 years ago by ★ 4.6k • written 2.4 years ago by • 0
0
votes
3
replies
1.9k
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub org.Hs.eg.db ensembldb
2.5 years ago • updated 2.4 years ago sandmann.t ▴ 70
1
vote
0
replies
1.1k
views
News: Ensembl 107 has been released
ensembldb
2.5 years ago Aleena ▴ 30
0
votes
1
reply
1.4k
views
bioMart Sscrofa_gene_ensembl getBM() paralogues ERROR
biomaRt ensembldb paralogues
updated 2.5 years ago by ★ 1.6k • written 2.5 years ago by • 0
0
votes
3
replies
3.8k
views
Can't Install ensembldb and EnsDb.Hsapiens.v86
installation EnsDb.Hsapiens.v86 Bioconductor package ensembldb
2.6 years ago • updated 2.5 years ago elmfinds • 0
2
votes
0
replies
918
views
News: News:Ensembl 106 has just been released!
ensembl biomaRt ensembldb
2.8 years ago Benjamin ▴ 30
2
votes
2
replies
1.5k
views
ensembldb to make the EnsDb for Human Version 105 using 'fetchTablesFromEnsembl' I'm on day two, can it be sped up?
ensembldb
2.9 years ago Matthew Thornton ▴ 380
0
votes
2
replies
3.4k
views
How to get the rsID of 4 million SNPA
ensembldb SNP SNPData genomes
written 2.9 years ago by • 0
9
votes
14
replies
7.9k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 6 months ago by 4.1k • written 3.0 years ago by ▴ 40
0
votes
2
replies
1.9k
views
Can't convert dog ensembl IDs into gene names
biomaRt ensembldb
updated 3.1 years ago by ★ 4.6k • written 3.1 years ago by • 0
0
votes
3
replies
1.7k
views
Error: package or namespace load failed for 'EnsDb.Mmusculus.v79'
EnsDb.Mmusculus.v79 EnsDb.Mmusculus.v75 ensembldb
updated 3.1 years ago by ★ 2.1k • written 3.1 years ago by • 0
1
vote
0
replies
990
views
News: Ensembl 105 has just been released!
ensembl biomaRt ensembldb
3.1 years ago mchakiachvili ▴ 20
0
votes
1
reply
1.3k
views
How to get Cytogenetic band for muscles gene by using Biomart or other tools in R
Annotation biomaRt ensembldb
written 3.2 years ago by • 0
10
votes
18
replies
3.5k
views
ensembldb support for Ensembl's transcript_name column
ensembldb
updated 3.2 years ago by 16k • written 3.2 years ago by 43k
0
votes
3
replies
1.4k
views
Problem select / ensembl package
ensembldb
3.2 years ago yinnahm • 0
2
votes
3
replies
2.1k
views
biomart query in R is not matching ensembl website - missing results
ensembldb biomaRt
updated 3.3 years ago by ★ 6.6k • written 3.3 years ago by • 0
0
votes
3
replies
1.3k
views
Error using old ensembldb annotations with R 4.0 +
anno EnsDb.Hsapiens.v79 ensDb.HSapiens.v92 AnnotationDbi ensembldb
3.4 years ago rbenel ▴ 40
1
vote
9
replies
2.5k
views
How to filter EnsDb into another EnsDb object instead of GRange?
ens ensembldb EnsDb.Hsapiens.v86 EnsDb.Rnorvegicus.v75
3.7 years ago Ahdee ▴ 50
1
vote
0
replies
1.3k
views
News: Ensembl 104 has just been released!
ensembldb biomaRt
3.7 years ago mchakiachvili ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Comment: EdgeR Biological CVs by James • 0
Thank you Gordon and Joseph. I presume question (1) would be answered by using a prior G0 of 0? For question (2), I was expecting a biolog…
Answer: EdgeR Biological CVs by Gordon Smyth 52k
I think your questions are answered by the published paper. You might also like to consult recent papers on edgeR by Yunshun Chen and Pedro…
Votes
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Awards • All
Popular Question to Gordon Smyth 52k
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Scholar to James W. MacDonald 67k
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