Showing : ensembldb • reset
2
votes
5
replies
140
views
get BM error
ensembldb
updated 23 hours ago by 65k • written 1 day ago by • 0
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 21 days ago by • 0 • written 5.4 years ago by ★ 3.9k
0
votes
1
reply
156
views
Convert transcriptomic bam to genomic bam?
ensembldb transcriptome genome coordinateconversion
updated 23 days ago by 41k • written 26 days ago by ▴ 10
0
votes
1
reply
216
views
Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 10 weeks ago by 65k • written 10 weeks ago by ▴ 10
2
votes
3
replies
291
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
10 weeks ago Kai Hu ▴ 70
1
vote
1
reply
213
views
502 error biomaRt getLDS()
ensembldb biomaRt
updated 10 weeks ago by • 0 • written 11 weeks ago by ▴ 10
2
votes
3
replies
482
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
758
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
541
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
6 months ago Rockbar • 0
0
votes
10
replies
819
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 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
477
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
1.5k
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
1.0k
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
681
views
BiomaRt - Problem to access homolog lists
biomaRt ensembldb
14 months ago ginie.dub • 0
1
vote
0
replies
643
views
News: Ensembl 109 has been released
ensembldb
14 months ago Aleena ▴ 20
0
votes
3
replies
967
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
720
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
812
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
771
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
19 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 19 months ago by ▴ 120 • written 19 months ago by ▴ 10
0
votes
1
reply
710
views
getBM Error with certain attribute combinations
biomaRt ensembldb
updated 20 months ago by ★ 4.0k • 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
795
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
22 months ago elmfinds • 0
2
votes
0
replies
711
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
2.6k
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
5.7k
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
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
782
views
News: Ensembl 105 has just been released!
ensembl biomaRt ensembldb
2.4 years ago mchakiachvili ▴ 20
0
votes
1
reply
951
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
997
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
996
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
3.1 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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Replies
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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