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Ensembl
•
reset
5
votes
3
replies
286
views
Problem obtaining NCBI gene IDs from Ensembl version 107
biomaRt
ensembldb
ensembl
3 months ago • updated 15 days ago
jamie.gearing
▴ 60
1
vote
2
replies
199
views
News:
Ensembl 108 has been released!
biomaRt
ensembldb
ensembl
written 3 months ago by
Louisse
▴ 10
0
votes
0
replies
214
views
biomaRt, Ensembl, retrieve "Phenotypes" information
Ensembl
biomaRt
5 months ago
Hector
• 0
5
votes
4
replies
2.4k
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
updated 10 weeks ago by
SE
• 0 • written 9 months ago by
kieran.short
▴ 30
2
votes
0
replies
309
views
News:
News:Ensembl 106 has just been released!
ensembl
biomaRt
ensembldb
9 months ago
Benjamin
▴ 20
2
votes
3
replies
622
views
Ensembl non responsive
ensembl
R
9 months ago
ksci
▴ 10
2
votes
1
reply
384
views
Can Rsubread output use Ensembl gene IDs
Ensembl
Rsubread
updated 10 months ago by
Gordon Smyth
47k • written 10 months ago by
agustin.gonvi
▴ 10
8
votes
9
replies
2.1k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 12 months ago by
Hervé Pagès
16k • written 12 months ago by
jon.klonowski
▴ 40
0
votes
3
replies
543
views
biomaRT getBM() get stuck
biomaRt
getbm
ensembl
updated 12 months ago by
Mike Smith
★ 5.8k • written 12 months ago by
Ariel Simon
• 0
1
vote
0
replies
348
views
News:
Ensembl 105 has just been released!
ensembl
biomaRt
ensembldb
13 months ago
mchakiachvili
▴ 20
15
votes
13
replies
1.4k
views
celldex ensembl gene annotation issue
SingleR
celldex
HumanPrimaryCellAtlasData
ensembl
updated 14 months ago by
xiang
▴ 10 • written 14 months ago by
immuno.dh
▴ 20
0
votes
6
replies
828
views
Getting paralogus genes from biomart for mouse
biomart
biomaRt
Ensembl
updated 18 months ago by
Kevin Blighe
3.7k • written 18 months ago by
hemantcnaik
• 0
0
votes
2
replies
776
views
News:
Ensembl 103 has been released
biomaRt
ensembldb
Ensembl
ensemblVEP
Biomart
23 months ago • updated 21 months ago
mchakiachvili
▴ 20
1
vote
1
reply
633
views
topGO question
Ensembl
ensembldb
updated 2.1 years ago by
James W. MacDonald
62k • written 2.1 years ago by
H. Stotz
• 0
0
votes
0
replies
449
views
News:
Ensembl 102 has been released
Ensembl
biomaRt
BioMar
ensembldb
2.2 years ago
mchakiachvili
▴ 20
4
votes
8
replies
9.8k
views
Ensembl site unresponsive
ensembl
biomart
updated 21 months ago by
tommaso.gastaldi
• 0 • written 2.3 years ago by
lirongrossmann
▴ 40
2
votes
11
replies
3.8k
views
biomaRT connexion problem make failed my unit tests
biomaRt
Peer's Certificate
Ensembl
updated 24 months ago by
Mike Smith
★ 5.8k • written 2.3 years ago by
ilysR
• 0
4
votes
17
replies
1.4k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt
annotation
Ensembl
annotationHub
updated 2.4 years ago by
Kevin Blighe
3.7k • written 2.4 years ago by
Didi
▴ 10
0
votes
1
reply
575
views
News:
Ensembl 101 hase been released
Ensembl
BioMart
News
2.4 years ago
mchakiachvili
▴ 20
1
vote
3
replies
1.2k
views
Convert mouse gene ids to hamster gene ids
biomart
R
ensembl
updated 21 months ago by
Kevin Blighe
3.7k • written 2.5 years ago by
rykerklie7
• 0
1
vote
0
replies
579
views
News:
ensembldb EnsDb databases for Ensembl release 100 added to AnnotationHub
ensembl
annotation
ensembldb
News
2.7 years ago
Johannes Rainer
★ 2.0k
1
vote
0
replies
381
views
News:
Ensembl 100 has been released
biomart
ensembl
e100
mart
news
News
2.7 years ago
Thomas Maurel
▴ 790
0
votes
4
replies
532
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 2.8 years ago by
Michael Love
39k • written 2.8 years ago by
slouis
• 0
1
vote
2
replies
1.0k
views
getBM biomart ensembl Error report
biomaRt
ensembl
updated 2.8 years ago by
Mike Smith
★ 5.8k • written 2.8 years ago by
nina.hahn
• 0
0
votes
1
reply
962
views
ChIPSeeker with Ensembl IDs
chipseeker
Ensembl
EnsDb.Mmusculus.v79
ensembldb
2.8 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
800
views
Error in martCheck(mart, c("ensembl", "ENSEMBL_MART_ENSEMBL")) : No dataset selected, please select a dataset first.
biomart
mart
ensembl
updated 2.8 years ago by
James W. MacDonald
62k • written 2.8 years ago by
didemdkn
• 0
0
votes
0
replies
290
views
News:
Changes to BioMart in Ensembl release 100 and Ensembl Genomes release 47
biomaRt
Ensembl
News
2.9 years ago
Astrid_Ensembl
• 0
4
votes
4
replies
844
views
biomaRt getSequence fails with genomic coordinates
biomart
getSequence
genomic coordinates
ENSEMBL
bug report
updated 3.0 years ago by
Mike Smith
★ 5.8k • written 3.0 years ago by
Ni-Ar
▴ 10
0
votes
1
reply
280
views
Question regarding retrieving miRNA sequences from ENSEMBLE
ensembl
updated 3.0 years ago by
Michael Love
39k • written 3.0 years ago by
mohsamir2016
• 0
0
votes
0
replies
416
views
News:
Ensembl 99 has been released and renaming of species
biomart
ensembl
e99
mart
news
News
3.0 years ago
Thomas Maurel
▴ 790
4
votes
11
replies
922
views
Dealing with duplicated genes in camera gene set testing
limma
camera
gene set testing
ensembl
updated 3.1 years ago by
Robert Castelo
★ 3.0k • written 3.1 years ago by
Jeremy Beales
▴ 10
1
vote
3
replies
1.6k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub
Ensembl
Mouse
AnnotationHub Ensembl
3.1 years ago
dmgatti
▴ 10
0
votes
14
replies
805
views
Error while opening Mart with biomaRt package
software error
ensembl
biomart
3.1 years ago
loicborcard01
• 0
0
votes
6
replies
463
views
Anyone else having trouble with biomaRt (Oct 10, 2019)
ensembl
biomaRt
updated 3.3 years ago by
Mike Smith
★ 5.8k • written 3.3 years ago by
swbarnes2
★ 1.2k
0
votes
7
replies
1.4k
views
BioMart does not find mouse homologs of human genes
biomart
homolog
ortholog
gene conversion
ensembl
updated 3.3 years ago by
James W. MacDonald
62k • written 3.3 years ago by
atakanekiz
▴ 30
0
votes
0
replies
509
views
News:
Ensembl 98 has been released and renaming of species
biomart
ensembl
e98
mart
News
3.3 years ago
Thomas Maurel
▴ 790
0
votes
1
reply
380
views
Eliminate redundancy in biomaRt (2.38.0) query
biomaRt
Ensembl
updated 3.5 years ago by
Mike Smith
★ 5.8k • written 3.5 years ago by
olibee1315
• 0
0
votes
3
replies
704
views
external_gene_id attribute removed from new biomaRt version
biomaRt
Ensembl
Ensemblplants
3.5 years ago
Didi
▴ 10
1
vote
0
replies
526
views
News:
ensembldb EnsDb databases for Ensembl release 97 added to AnnotationHub
annotation
ensembldb
Ensembl
News
3.6 years ago
Johannes Rainer
★ 2.0k
1
vote
0
replies
430
views
News:
Ensembl 97 has been released
biomart
ensembl
e97
News
3.6 years ago
James Allen
▴ 10
10
votes
8
replies
1.6k
views
Best alternative annotation package to BiomaRt
R
biomaRt
Ensembl
rnaseq
3.6 years ago
m93
▴ 10
0
votes
1
reply
680
views
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string
biomart
ensembl
R
Bioconductor
3.6 years ago
lbuo
• 0
0
votes
4
replies
884
views
Error message: "Request to BioMart web service failed."
BiocManager
biomaRt
listMarts()
ensembl
Biomart
updated 3.6 years ago by
Mike Smith
★ 5.8k • written 3.6 years ago by
ktd2918
• 0
3
votes
2
replies
697
views
GEO Download - "The query to BioMart webservice returned an invalid result..."
biomart
geo
software error
ensembl
updated 3.6 years ago by
Mike Smith
★ 5.8k • written 3.6 years ago by
wes
▴ 10
1
vote
1
reply
520
views
Gene biotype for a given symbol
ensembl
updated 3.6 years ago by
Johannes Rainer
★ 2.0k • written 3.6 years ago by
adai
• 0
1
vote
3
replies
1.1k
views
Scan error using biomart getBM with version option and host set
biomart
ensembl
getbm
3.7 years ago
Marc Saric
▴ 70
2
votes
0
replies
536
views
News:
ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
updated 3.7 years ago by
nguyenlieuduoc
• 0 • written 3.7 years ago by
shepherl
3.4k
6
votes
5
replies
3.5k
views
biomaRt Ensembl gene ID to multiple HGNC symbol
ensembl
symbol
hgnc
biomart
updated 3.7 years ago by
James W. MacDonald
62k • written 3.7 years ago by
foehn
▴ 80
0
votes
0
replies
447
views
News:
Ensembl 96 has been released
ensembl
biomart
biomaRt
e96
news
News
3.8 years ago
amonida
▴ 20
4
votes
5
replies
929
views
Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens.UCSC.hg19.knownGene
ensembl
cdschrom
org.Hs.eg.db
AnnotationDbi
SingleCellExperiment
updated 3.8 years ago by
James W. MacDonald
62k • written 3.8 years ago by
kushshah
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I felt that my way of analyzing this data set was a bit unfortunate. I was not involved in the experimental design myself and am now trying…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
For tissue T1 and each time point, each replicate corresponds to a single plant. For tissue T2, we actually had to sample 5 plants per rep…
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
> Due to the high degree of heterozygosity of the plants used for the experiment, we thought it best to pool the same tissue under the same…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
How many plants are used for each of the biological replicate samples? One plant or a few?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
Yes you are right, we have 24 RNA-seq libraries in total. The replicates come from the same population of plants, but independent from tho…
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on which data type limma::removeBatchEffect can be applyed?
How can I draw a barplot of complexheatmap according 'Tumor Type'
on which data type limma::removeBatchEffect can be applyed?
DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
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