Showing : ensembldb • reset
2
votes
5
replies
255
views
get BM error
ensembldb
updated 10 days ago by 65k • written 10 days ago by • 0
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 4 weeks ago by • 0 • written 5.5 years ago by ★ 3.9k
0
votes
1
reply
171
views
Convert transcriptomic bam to genomic bam?
ensembldb transcriptome genome coordinateconversion
updated 4 weeks ago by 41k • written 5 weeks ago by ▴ 10
0
votes
1
reply
225
views
Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 11 weeks ago by 65k • written 12 weeks ago by ▴ 10
2
votes
3
replies
314
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
12 weeks ago Kai Hu ▴ 70
1
vote
1
reply
227
views
502 error biomaRt getLDS()
ensembldb biomaRt
updated 11 weeks ago by • 0 • written 12 weeks ago by ▴ 10
2
votes
3
replies
503
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio cDNA ensembldb NCBI
5 months ago R_Page • 0
2
votes
5
replies
797
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
6 months ago • updated 5 months ago j_denton • 0
0
votes
4
replies
561
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
6 months ago Rockbar • 0
0
votes
10
replies
841
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
4.1k
views
Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 6 months ago by 690 • written 21 months ago by ▴ 20
3
votes
1
reply
1.4k
views
Mouse to Human Genes using bioconductor
ensembldb
updated 9 months ago by 65k • written 9 months ago by ▴ 10
0
votes
1
reply
487
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 9 months ago by 65k • written 9 months ago by • 0
0
votes
1
reply
1.5k
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
1.1k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt ensembldb RNA ensembl
updated 13 months ago by ★ 2.0k • written 13 months ago by • 0
0
votes
0
replies
695
views
BiomaRt - Problem to access homolog lists
biomaRt ensembldb
14 months ago ginie.dub • 0
1
vote
0
replies
653
views
News: Ensembl 109 has been released
ensembldb
15 months ago Aleena ▴ 20
0
votes
3
replies
984
views
Uniprot IDs and NCBI taxonomy IDs to coding sequences
ensembldb biodbUniprot
updated 15 months ago by 65k • written 15 months ago by • 0
2
votes
4
replies
735
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
836
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
778
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 19 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
19 months ago dario.beraldi • 0
2
votes
3
replies
2.3k
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
0
votes
1
reply
715
views
getBM Error with certain attribute combinations
biomaRt ensembldb
updated 20 months ago by ★ 4.1k • written 20 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
21 months ago • updated 20 months ago sandmann.t ▴ 70
1
vote
0
replies
808
views
News: Ensembl 107 has been released
ensembldb
22 months ago Aleena ▴ 20
0
votes
1
reply
1.0k
views
bioMart Sscrofa_gene_ensembl getBM() paralogues ERROR
biomaRt ensembldb paralogues
updated 22 months ago by ★ 1.6k • written 22 months ago by • 0
0
votes
3
replies
2.9k
views
Can't Install ensembldb and EnsDb.Hsapiens.v86
installation EnsDb.Hsapiens.v86 Bioconductor package ensembldb
22 months ago elmfinds • 0
2
votes
0
replies
719
views
News: News:Ensembl 106 has just been released!
ensembl biomaRt ensembldb
2.1 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
2.2 years ago Matthew Thornton ▴ 350
0
votes
2
replies
2.6k
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
5.8k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 7 weeks ago by 3.9k • written 2.3 years ago by ▴ 40
0
votes
2
replies
1.4k
views
Can't convert dog ensembl IDs into gene names
biomaRt ensembldb
updated 2.4 years ago by ★ 4.1k • written 2.4 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 2.4 years ago by ★ 2.0k • written 2.4 years ago by • 0
1
vote
0
replies
794
views
News: Ensembl 105 has just been released!
ensembl biomaRt ensembldb
2.4 years ago mchakiachvili ▴ 20
0
votes
1
reply
966
views
How to get Cytogenetic band for muscles gene by using Biomart or other tools in R
Annotation biomaRt ensembldb
written 2.5 years ago by • 0
10
votes
18
replies
2.9k
views
ensembldb support for Ensembl's transcript_name column
ensembldb
updated 2.5 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 2.6 years ago by ★ 6.5k • written 2.6 years ago by • 0
0
votes
3
replies
1.0k
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
1.0k
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 3.1 years ago by ★ 2.0k • written 3.1 years ago by ▴ 510
1
vote
2
replies
1.1k
views
Unable to use ensembldb's "ensDbFromGff()" function on .gff file from NCBI
ensembldb RNASeq
3.1 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
2.5k
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
50 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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