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Ensembl
•
reset
1
vote
2
replies
212
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl
R
biomaRt
10 weeks ago • updated 9 weeks ago
Miguel
• 0
7
votes
25
replies
3.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 25 days ago by
Bruno
• 0 • written 4.9 years ago by
Guido Hooiveld
★ 3.7k
0
votes
2
replies
454
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt
ensembldb
RNA
ensembl
updated 6 months ago by
Johannes Rainer
★ 2.0k • written 6 months ago by
Christopher
• 0
5
votes
3
replies
876
views
Problem obtaining NCBI gene IDs from Ensembl version 107
biomaRt
ensembldb
ensembl
11 months ago • updated 8 months ago
jamie.gearing
▴ 60
1
vote
2
replies
515
views
News:
Ensembl 108 has been released!
biomaRt
ensembldb
ensembl
written 11 months ago by
Louisse
▴ 10
0
votes
0
replies
430
views
biomaRt, Ensembl, retrieve "Phenotypes" information
Ensembl
biomaRt
13 months ago
Hector
• 0
7
votes
4
replies
4.8k
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
updated 10 months ago by
SE
▴ 10 • written 17 months ago by
kieran.short
▴ 40
2
votes
0
replies
523
views
News:
News:Ensembl 106 has just been released!
ensembl
biomaRt
ensembldb
17 months ago
Benjamin
▴ 20
2
votes
3
replies
986
views
Ensembl non responsive
ensembl
R
18 months ago
ksci
▴ 20
2
votes
1
reply
753
views
Can Rsubread output use Ensembl gene IDs
Ensembl
Rsubread
updated 18 months ago by
Gordon Smyth
48k • written 18 months ago by
agustin.gonvi
▴ 20
8
votes
9
replies
4.1k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 20 months ago by
Hervé Pagès
16k • written 20 months ago by
jon.klonowski
▴ 40
0
votes
3
replies
971
views
biomaRT getBM() get stuck
biomaRt
getbm
ensembl
updated 21 months ago by
Mike Smith
★ 6.1k • written 21 months ago by
Ariel Simon
• 0
1
vote
0
replies
619
views
News:
Ensembl 105 has just been released!
ensembl
biomaRt
ensembldb
22 months ago
mchakiachvili
▴ 20
15
votes
13
replies
2.3k
views
celldex ensembl gene annotation issue
SingleR
celldex
HumanPrimaryCellAtlasData
ensembl
updated 23 months ago by
xiang
▴ 10 • written 23 months ago by
immuno.dh
▴ 20
0
votes
6
replies
1.4k
views
Getting paralogus genes from biomart for mouse
biomart
biomaRt
Ensembl
updated 2.2 years ago by
Kevin Blighe
3.8k • written 2.2 years ago by
hemantcnaik
• 0
0
votes
2
replies
1.1k
views
News:
Ensembl 103 has been released
biomaRt
ensembldb
Ensembl
ensemblVEP
Biomart
2.6 years ago • updated 2.4 years ago
mchakiachvili
▴ 20
1
vote
1
reply
1.0k
views
topGO question
Ensembl
ensembldb
updated 2.8 years ago by
James W. MacDonald
63k • written 2.8 years ago by
H. Stotz
• 0
0
votes
0
replies
621
views
News:
Ensembl 102 has been released
Ensembl
biomaRt
BioMar
ensembldb
2.8 years ago
mchakiachvili
▴ 20
4
votes
8
replies
12k
views
Ensembl site unresponsive
ensembl
biomart
updated 2.5 years ago by
tommaso.gastaldi
• 0 • written 3.0 years ago by
lirongrossmann
▴ 40
2
votes
11
replies
5.0k
views
biomaRT connexion problem make failed my unit tests
biomaRt
Peer's Certificate
Ensembl
updated 2.7 years ago by
Mike Smith
★ 6.1k • written 3.0 years ago by
ilysR
• 0
4
votes
17
replies
2.0k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt
annotation
Ensembl
annotationHub
updated 3.1 years ago by
Kevin Blighe
3.8k • written 3.1 years ago by
Didi
▴ 10
0
votes
1
reply
779
views
News:
Ensembl 101 hase been released
Ensembl
BioMart
News
3.1 years ago
mchakiachvili
▴ 20
1
vote
3
replies
2.0k
views
Convert mouse gene ids to hamster gene ids
biomart
R
ensembl
updated 7 months ago by
Kevin Blighe
3.8k • written 3.2 years ago by
rykerklie7
• 0
1
vote
0
replies
886
views
News:
ensembldb EnsDb databases for Ensembl release 100 added to AnnotationHub
ensembl
annotation
ensembldb
News
3.4 years ago
Johannes Rainer
★ 2.0k
1
vote
0
replies
622
views
News:
Ensembl 100 has been released
biomart
ensembl
e100
mart
news
News
3.4 years ago
Thomas Maurel
▴ 800
0
votes
4
replies
835
views
Having a hard time creating a Txi object from an existing Salmon output file to convert transcript file to gene id TPM
Salmon
tximport
tximportdata
ensembl
updated 3.5 years ago by
Michael Love
40k • written 3.5 years ago by
slouis
• 0
1
vote
2
replies
1.2k
views
getBM biomart ensembl Error report
biomaRt
ensembl
updated 3.5 years ago by
Mike Smith
★ 6.1k • written 3.5 years ago by
nina.hahn
▴ 10
0
votes
1
reply
1.3k
views
ChIPSeeker with Ensembl IDs
chipseeker
Ensembl
EnsDb.Mmusculus.v79
ensembldb
3.5 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
1.5k
views
Error in martCheck(mart, c("ensembl", "ENSEMBL_MART_ENSEMBL")) : No dataset selected, please select a dataset first.
biomart
mart
ensembl
updated 3.5 years ago by
James W. MacDonald
63k • written 3.5 years ago by
didemdkn
• 0
0
votes
0
replies
430
views
News:
Changes to BioMart in Ensembl release 100 and Ensembl Genomes release 47
biomaRt
Ensembl
News
3.6 years ago
Astrid_Ensembl
• 0
4
votes
4
replies
1.2k
views
biomaRt getSequence fails with genomic coordinates
biomart
getSequence
genomic coordinates
ENSEMBL
bug report
updated 3.6 years ago by
Mike Smith
★ 6.1k • written 3.6 years ago by
Ni-Ar
▴ 10
0
votes
1
reply
495
views
Question regarding retrieving miRNA sequences from ENSEMBLE
ensembl
updated 3.7 years ago by
Michael Love
40k • written 3.7 years ago by
mohsamir2016
• 0
0
votes
0
replies
563
views
News:
Ensembl 99 has been released and renaming of species
biomart
ensembl
e99
mart
news
News
3.7 years ago
Thomas Maurel
▴ 800
4
votes
11
replies
1.4k
views
Dealing with duplicated genes in camera gene set testing
limma
camera
gene set testing
ensembl
updated 3.8 years ago by
Robert Castelo
★ 3.0k • written 3.8 years ago by
Jeremy Beales
▴ 10
1
vote
3
replies
1.9k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub
Ensembl
Mouse
AnnotationHub Ensembl
3.8 years ago
dmgatti
▴ 10
0
votes
14
replies
1.2k
views
Error while opening Mart with biomaRt package
software error
ensembl
biomart
3.8 years ago
loicborcard01
• 0
0
votes
6
replies
714
views
Anyone else having trouble with biomaRt (Oct 10, 2019)
ensembl
biomaRt
updated 4.0 years ago by
Mike Smith
★ 6.1k • written 4.0 years ago by
swbarnes2
★ 1.3k
0
votes
7
replies
2.1k
views
BioMart does not find mouse homologs of human genes
biomart
homolog
ortholog
gene conversion
ensembl
updated 4.0 years ago by
James W. MacDonald
63k • written 4.0 years ago by
atakanekiz
▴ 30
0
votes
0
replies
702
views
News:
Ensembl 98 has been released and renaming of species
biomart
ensembl
e98
mart
News
4.0 years ago
Thomas Maurel
▴ 800
0
votes
1
reply
582
views
Eliminate redundancy in biomaRt (2.38.0) query
biomaRt
Ensembl
updated 4.2 years ago by
Mike Smith
★ 6.1k • written 4.2 years ago by
olibee1315
• 0
0
votes
3
replies
1.1k
views
external_gene_id attribute removed from new biomaRt version
biomaRt
Ensembl
Ensemblplants
4.2 years ago
Didi
▴ 10
1
vote
0
replies
680
views
News:
ensembldb EnsDb databases for Ensembl release 97 added to AnnotationHub
annotation
ensembldb
Ensembl
News
4.2 years ago
Johannes Rainer
★ 2.0k
1
vote
0
replies
634
views
News:
Ensembl 97 has been released
biomart
ensembl
e97
News
4.3 years ago
James Allen
▴ 10
10
votes
8
replies
2.2k
views
Best alternative annotation package to BiomaRt
R
biomaRt
Ensembl
rnaseq
4.3 years ago
m93
▴ 10
0
votes
1
reply
847
views
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string
biomart
ensembl
R
Bioconductor
4.3 years ago
lbuo
• 0
0
votes
4
replies
1.1k
views
Error message: "Request to BioMart web service failed."
BiocManager
biomaRt
listMarts()
ensembl
Biomart
updated 4.3 years ago by
Mike Smith
★ 6.1k • written 4.3 years ago by
ktd2918
• 0
3
votes
2
replies
927
views
GEO Download - "The query to BioMart webservice returned an invalid result..."
biomart
geo
software error
ensembl
updated 4.3 years ago by
Mike Smith
★ 6.1k • written 4.3 years ago by
wes
▴ 10
1
vote
1
reply
785
views
Gene biotype for a given symbol
ensembl
updated 4.3 years ago by
Johannes Rainer
★ 2.0k • written 4.3 years ago by
adai
• 0
1
vote
3
replies
1.3k
views
Scan error using biomart getBM with version option and host set
biomart
ensembl
getbm
4.4 years ago
Marc Saric
▴ 70
2
votes
0
replies
760
views
News:
ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
updated 4.4 years ago by
nguyenlieuduoc
• 0 • written 4.4 years ago by
shepherl
3.5k
50 results • Page
1 of 1
Recent ...
Replies
Comment: Exporting DESeq2 filtered results
by
James W. MacDonald
63k
I am interested to know what part of my response you found rude. I asked nicely that you don't add to ancient posts, said your post isn't r…
Comment: Speeding up of DelayedArray::write_block()
by
Hervé Pagès
16k
> I can imagine writing a sparse high-dimensional array in HDF5, but I'm still not sure how to implement the part where it is read and imme…
Comment: Speeding up of DelayedArray::write_block()
by
Hervé Pagès
16k
Not in BioC 3.18. At some point (e.g. in 6 months) they will be deprecated, then 6 months later (i.e. in 1 year) they will be defunct, then…
Comment: Biostrings error at retrieving protein sequences
by
Hervé Pagès
16k
Yes, but you need to put the clean names back on the AAStringSet object: ``` names(protein_sequences) <- gsub(" .*", "", names(protein_sequ…
Comment: Exporting DESeq2 filtered results
by
camillab.
▴ 10
thanks! I didn't`t notice that. I will cancel it now!
Votes
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
A: BiomaRt Arabidopsis genome unavailable
Answer: enrichKEGG
A: Effect of lfcThreshold on p-value in DESeq2
Comment: Mixed up sample info with plotPCA
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