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ensembldb
•
reset
2
votes
4
replies
396
views
seqlevelsStyle() not working
ensembldb
genomei
GenomeInfoDb
written 3 months ago by
Kai Hu
▴ 70
8
votes
41
replies
5.9k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 3 days ago by
Daniele
• 0 • written 5.5 years ago by
Guido Hooiveld
★ 4.0k
1
vote
0
replies
87
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
10 days ago
Aleena
▴ 30
2
votes
5
replies
337
views
get BM error
ensembldb
updated 4 weeks ago by
James W. MacDonald
66k • written 4 weeks ago by
Fara
• 0
0
votes
1
reply
199
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 7 weeks ago by
Michael Love
42k • written 8 weeks ago by
saadmurtazakhan
▴ 10
9
votes
11
replies
6.0k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 10 weeks ago by
shepherl
3.9k • written 2.3 years ago by
jon.klonowski
▴ 40
1
vote
1
reply
251
views
502 error biomaRt getLDS()
ensembldb
biomaRt
updated 3 months ago by
Robin
• 0 • written 3 months ago by
Pez
▴ 10
0
votes
1
reply
251
views
Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene
ensembldb
GenomicFeatures
Mus_musculus
updated 3 months ago by
James W. MacDonald
66k • written 3 months ago by
ramonmassoni
▴ 10
0
votes
2
replies
2.7k
views
How to get the rsID of 4 million SNPA
ensembldb
SNP
SNPData
genomes
written 2.2 years ago by
Weiqiong
• 0
2
votes
3
replies
529
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
0
votes
1
reply
1.0k
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
Lillian
• 0
2
votes
5
replies
876
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio
convert
ensembldb
NCBI
6 months ago
j_denton
• 0
0
votes
4
replies
593
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO
ensembldb
7 months ago
Rockbar
• 0
7
votes
6
replies
4.3k
views
Conversion of UniProt to Ensembl
biomaRt
ensembldb
UniProt.ws
updated 7 months ago by
Marcel Ramos
700 • written 21 months ago by
Recep
▴ 20
0
votes
10
replies
866
views
ensembldb::getGenomeTwoBitFile() not working for many species
AnnotationHubSoftware
ensembldb
updated 8 months ago by
James W. MacDonald
66k • written 8 months ago by
cjag
• 0
3
votes
1
reply
1.5k
views
Mouse to Human Genes using bioconductor
ensembldb
updated 9 months ago by
James W. MacDonald
66k • written 9 months ago by
Max
▴ 10
0
votes
1
reply
510
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread
ensembldb
updated 9 months ago by
James W. MacDonald
66k • written 9 months ago by
Ya
• 0
0
votes
1
reply
1.6k
views
News:
News:Ensembl 110 has been released
ensembldb
biomaRt
updated 10 months ago by
Michael Love
42k • written 10 months ago by
Benjamin
▴ 30
0
votes
2
replies
1.1k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt
ensembldb
RNA
ensembl
updated 13 months ago by
Johannes Rainer
★ 2.0k • written 13 months ago by
Christopher
• 0
0
votes
0
replies
719
views
BiomaRt - Problem to access homolog lists
biomaRt
ensembldb
15 months ago
ginie.dub
• 0
1
vote
0
replies
685
views
News:
Ensembl 109 has been released
ensembldb
15 months ago
Aleena
▴ 30
0
votes
3
replies
1.0k
views
Uniprot IDs and NCBI taxonomy IDs to coding sequences
ensembldb
biodbUniprot
updated 16 months ago by
James W. MacDonald
66k • written 16 months ago by
Peter
• 0
2
votes
3
replies
1.8k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal
ensembldb
rtracklayer
Annotation
updated 16 months ago by
rbj
• 0 • written 18 months ago by
Jake
▴ 10
2
votes
4
replies
752
views
Successor of genesBy Defunct Function
ensembldb
updated 16 months ago by
Hervé Pagès
16k • written 16 months ago by
Dario Strbenac
★ 1.5k
5
votes
3
replies
1.5k
views
Problem obtaining NCBI gene IDs from Ensembl version 107
biomaRt
ensembldb
ensembl
19 months ago • updated 16 months ago
jamie.gearing
▴ 60
1
vote
3
replies
864
views
Convert Chromosome postion to gene symbol
biomaRt
ensembldb
17 months ago
mbansal
• 0
1
vote
2
replies
793
views
News:
Ensembl 108 has been released!
biomaRt
ensembldb
ensembl
written 19 months ago by
Louisse
▴ 10
0
votes
5
replies
2.1k
views
Error when annotating ENSEMBLE transcript IDs from chicken annotation DB
R
ensembldb
Annotation
updated 19 months ago by
Guido Hooiveld
★ 4.0k • written 19 months ago by
Mohamed
▴ 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
20 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 20 months ago by
merv
▴ 120 • written 20 months ago by
simone.nevills
▴ 10
0
votes
1
reply
725
views
getBM Error with certain attribute combinations
biomaRt
ensembldb
updated 21 months ago by
ATpoint
★ 4.2k • written 21 months ago by
Luisa
• 0
0
votes
3
replies
1.3k
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub
org.Hs.eg.db
ensembldb
22 months ago • updated 21 months ago
sandmann.t
▴ 70
4
votes
4
replies
2.7k
views
Retrieve canonical transcript for each gene via ensembldb R package
annotation
ensembldb
updated 22 months ago by
jon.klonowski
▴ 40 • written 5.3 years ago by
simon.boutry
• 0
1
vote
0
replies
828
views
News:
Ensembl 107 has been released
ensembldb
22 months ago
Aleena
▴ 30
0
votes
1
reply
1.0k
views
bioMart Sscrofa_gene_ensembl getBM() paralogues ERROR
biomaRt
ensembldb
paralogues
updated 22 months ago by
Malcolm Cook
★ 1.6k • written 22 months ago by
Zeroual
• 0
0
votes
3
replies
3.0k
views
Can't Install ensembldb and EnsDb.Hsapiens.v86
installation
EnsDb.Hsapiens.v86
Bioconductor
package
ensembldb
23 months ago
elmfinds
• 0
2
votes
0
replies
729
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
▴ 360
0
votes
2
replies
1.4k
views
Can't convert dog ensembl IDs into gene names
biomaRt
ensembldb
updated 2.4 years ago by
ATpoint
★ 4.2k • written 2.4 years ago by
4214811
• 0
0
votes
3
replies
1.4k
views
Error: package or namespace load failed for 'EnsDb.Mmusculus.v79'
EnsDb.Mmusculus.v79
EnsDb.Mmusculus.v75
ensembldb
updated 2.4 years ago by
Johannes Rainer
★ 2.0k • written 2.4 years ago by
kelvin
• 0
1
vote
0
replies
807
views
News:
Ensembl 105 has just been released!
ensembl
biomaRt
ensembldb
2.5 years ago
mchakiachvili
▴ 20
10
votes
18
replies
2.9k
views
ensembldb support for Ensembl's transcript_name column
ensembldb
updated 2.5 years ago by
Hervé Pagès
16k • written 2.6 years ago by
Michael Love
42k
0
votes
3
replies
1.1k
views
Problem select / ensembl package
ensembldb
2.6 years ago
yinnahm
• 0
2
votes
3
replies
1.8k
views
biomart query in R is not matching ensembl website - missing results
ensembldb
biomaRt
updated 2.6 years ago by
Mike Smith
★ 6.5k • written 2.6 years ago by
Alice
• 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
2.8 years ago
rbenel
▴ 40
1
vote
9
replies
2.0k
views
How to filter EnsDb into another EnsDb object instead of GRange?
ens
ensembldb
EnsDb.Hsapiens.v86
EnsDb.Rnorvegicus.v75
3.0 years ago
Ahdee
▴ 50
1
vote
0
replies
1.0k
views
News:
Ensembl 104 has just been released!
ensembldb
biomaRt
3.1 years ago
mchakiachvili
▴ 20
0
votes
2
replies
1.4k
views
News:
Ensembl 103 has been released
biomaRt
ensembldb
Ensembl
ensemblVEP
Biomart
3.3 years ago • updated 3.1 years ago
mchakiachvili
▴ 20
2
votes
1
reply
1.5k
views
Retrieve gene description with ensembldb
biomaRt
ensembldb
AnnotationData
updated 3.1 years ago by
Johannes Rainer
★ 2.0k • written 3.1 years ago by
António Miguel de Jesus Domingues
▴ 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
50 results • Page
1 of 1
Recent ...
Replies
Comment: Volcano plot of scRNA-seq data not "centered"
by
tjl
• 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Answer: GSVA function
by
Robert Castelo
★ 3.3k
Hi, We recommend to input normalized expression values in logarithmic scale to GSVA. We also recommend to use the latest release of the …
Comment: Cannot install oligo on Fedora
by
Guido Hooiveld
★ 4.0k
Aha, that is a good one! Starting from release 40, as I just found out, Fedora apparently is not including/using `zlib` as such anymore, b…
Votes
Answer: How to run allelic imbalance in apeglm
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
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