Showing : Ensembldb • reset
0
votes
4
replies
616
views
Biomart and ensembl not working?
ensembldb biomaRt
updated 6 weeks ago by 68k • written 6 weeks ago by • 0
0
votes
0
replies
366
views
News: Ensembl 113 has been released
ensembl ensembldb mart biomaRt
4 months ago Ensembl_Jorge • 0
1
vote
3
replies
1.2k
views
502 error biomaRt getLDS()
ensembldb biomaRt
updated 6 months ago by 68k • written 13 months ago by ▴ 10
0
votes
0
replies
384
views
Job: Ensembl Job Vacancies
genomes Annotation GenomicVariation ensembldb
6 months ago Aleena ▴ 30
1
vote
1
reply
657
views
biomaRt getSequence(): Error in .lock2
ensembldb getSequence
updated 7 months ago by ★ 6.6k • written 7 months ago by ▴ 10
1
vote
0
replies
590
views
News: Ensembl 112 has been released.
ensembldb biomaRt ensemblrelease
9 months ago Aleena ▴ 30
2
votes
5
replies
713
views
get BM error
ensembldb
updated 10 months ago by 68k • written 10 months ago by • 0
10
votes
41
replies
7.9k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 9 months ago by • 0 • written 6.3 years ago by ★ 4.1k
0
votes
1
reply
532
views
Convert transcriptomic bam to genomic bam?
ensembldb transcriptome genome coordinateconversion
updated 11 months ago by 43k • written 11 months ago by ▴ 10
0
votes
1
reply
667
views
Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 12 months ago by 68k • written 12 months ago by ▴ 10
2
votes
4
replies
1.2k
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
written 12 months ago by ▴ 70
2
votes
3
replies
836
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio cDNA ensembldb NCBI
15 months ago R_Page • 0
4
votes
6
replies
2.3k
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
updated 5 months ago by • 0 • written 16 months ago by • 0
0
votes
4
replies
1.2k
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
16 months ago Rockbar • 0
0
votes
10
replies
1.4k
views
ensembldb::getGenomeTwoBitFile() not working for many species
AnnotationHubSoftware ensembldb
updated 17 months ago by 68k • written 17 months ago by • 0
7
votes
6
replies
7.1k
views
Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 16 months ago by 700 • written 2.6 years ago by ▴ 20
3
votes
1
reply
4.4k
views
Mouse to Human Genes using bioconductor
ensembldb
updated 19 months ago by 68k • written 19 months ago by ▴ 10
0
votes
1
reply
821
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
1
reply
2.7k
views
News: News:Ensembl 110 has been released
ensembldb biomaRt
updated 19 months ago by 43k • written 19 months ago by ▴ 30
0
votes
2
replies
1.8k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt ensembldb RNA ensembl
updated 23 months ago by ★ 2.1k • written 23 months ago by • 0
0
votes
0
replies
981
views
BiomaRt - Problem to access homolog lists
biomaRt ensembldb
2.1 years ago ginie.dub • 0
1
vote
0
replies
968
views
News: Ensembl 109 has been released
ensembldb
2.1 years ago Aleena ▴ 30
0
votes
3
replies
1.5k
views
Uniprot IDs and NCBI taxonomy IDs to coding sequences
ensembldb biodbUniprot
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
2
votes
4
replies
1.1k
views
Successor of genesBy Defunct Function
ensembldb
updated 2.1 years ago by 16k • written 2.1 years ago by ★ 1.6k
5
votes
3
replies
2.2k
views
Problem obtaining NCBI gene IDs from Ensembl version 107
biomaRt ensembldb ensembl
2.4 years ago • updated 2.1 years ago jamie.gearing ▴ 60
1
vote
3
replies
1.3k
views
Convert Chromosome postion to gene symbol
biomaRt ensembldb
2.2 years ago mbansal • 0
2
votes
3
replies
2.5k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal ensembldb rtracklayer Annotation
updated 2.1 years ago by • 0 • written 2.3 years ago by ▴ 10
1
vote
2
replies
1.1k
views
News: Ensembl 108 has been released!
biomaRt ensembldb ensembl
written 2.4 years ago by ▴ 10
0
votes
5
replies
2.9k
views
Error when annotating ENSEMBLE transcript IDs from chicken annotation DB
R ensembldb Annotation
updated 2.4 years ago by ★ 4.1k • written 2.4 years ago by ▴ 30
0
votes
4
replies
1.5k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
2.4 years ago dario.beraldi • 0
2
votes
3
replies
3.3k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 2.4 years ago by ▴ 150 • written 2.4 years ago by ▴ 10
0
votes
1
reply
933
views
getBM Error with certain attribute combinations
biomaRt ensembldb
updated 2.5 years ago by ★ 4.7k • written 2.5 years ago by • 0
0
votes
3
replies
2.0k
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub org.Hs.eg.db ensembldb
2.6 years ago • updated 2.5 years ago sandmann.t ▴ 70
1
vote
0
replies
1.1k
views
News: Ensembl 107 has been released
ensembldb
2.6 years ago Aleena ▴ 30
0
votes
1
reply
1.5k
views
bioMart Sscrofa_gene_ensembl getBM() paralogues ERROR
biomaRt ensembldb paralogues
updated 2.7 years ago by ★ 1.6k • written 2.7 years ago by • 0
0
votes
3
replies
4.0k
views
Can't Install ensembldb and EnsDb.Hsapiens.v86
installation EnsDb.Hsapiens.v86 Bioconductor package ensembldb
2.7 years ago elmfinds • 0
2
votes
0
replies
945
views
News: News:Ensembl 106 has just been released!
ensembl biomaRt ensembldb
2.9 years ago Benjamin ▴ 30
2
votes
2
replies
1.6k
views
ensembldb to make the EnsDb for Human Version 105 using 'fetchTablesFromEnsembl' I'm on day two, can it be sped up?
ensembldb
3.0 years ago Matthew Thornton ▴ 380
0
votes
2
replies
3.6k
views
How to get the rsID of 4 million SNPA
ensembldb SNP SNPData genomes
written 3.0 years ago by • 0
9
votes
14
replies
8.3k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 7 months ago by 4.1k • written 3.1 years ago by ▴ 40
0
votes
2
replies
1.9k
views
Can't convert dog ensembl IDs into gene names
biomaRt ensembldb
updated 3.2 years ago by ★ 4.7k • written 3.2 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 3.2 years ago by ★ 2.1k • written 3.2 years ago by • 0
1
vote
0
replies
1.0k
views
News: Ensembl 105 has just been released!
ensembl biomaRt ensembldb
3.2 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 3.3 years ago by • 0
10
votes
18
replies
3.7k
views
ensembldb support for Ensembl's transcript_name column
ensembldb
updated 3.3 years ago by 16k • written 3.4 years ago by 43k
0
votes
3
replies
1.5k
views
Problem select / ensembl package
ensembldb
3.4 years ago yinnahm • 0
2
votes
3
replies
2.2k
views
biomart query in R is not matching ensembl website - missing results
ensembldb biomaRt
updated 3.4 years ago by ★ 6.6k • written 3.4 years ago by • 0
0
votes
3
replies
1.4k
views
Error using old ensembldb annotations with R 4.0 +
anno EnsDb.Hsapiens.v79 ensDb.HSapiens.v92 AnnotationDbi ensembldb
3.6 years ago rbenel ▴ 40
1
vote
9
replies
2.6k
views
How to filter EnsDb into another EnsDb object instead of GRange?
ens ensembldb EnsDb.Hsapiens.v86 EnsDb.Rnorvegicus.v75
3.8 years ago Ahdee ▴ 50
1
vote
0
replies
1.3k
views
News: Ensembl 104 has just been released!
ensembldb biomaRt
3.8 years ago mchakiachvili ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840
Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Votes
A: What is the "linear model" part used for in Limma?
Comment: Use of limma R package with targeted proteomics for DE analysis
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
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