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Showing :
Ensembl
•
reset
15
votes
13
replies
778
views
celldex ensembl gene annotation issue
SingleR
celldex
HumanPrimaryCellAtlasData
ensembl
updated 6 months ago by
xiang
▴ 10 • written 6 months ago by
immuno.dh
▴ 20
14
votes
7
replies
7.5k
views
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2
ensembl
updated 4.3 years ago by
James W. MacDonald
59k • written 4.3 years ago by
casey.rimland
▴ 140
13
votes
8
replies
13k
views
how to use biomaRt with ensembl build 37
biomaRt
ensembl
GRCh37
updated 7.6 years ago by
Thomas Maurel
▴ 790 • written 7.6 years ago by
Pablo marin-garcia
▴ 90
10
votes
8
replies
1.3k
views
Best alternative annotation package to BiomaRt
R
biomaRt
Ensembl
rnaseq
2.9 years ago
m93
▴ 10
9
votes
1
reply
1.7k
views
News:
Ensembl release 80 is out!
biomart
Ensembl
zebrafish
Rat
1000 genomes phase 3
News
updated 7.0 years ago by
Sonali Arora
▴ 380 • written 7.0 years ago by
Thomas Maurel
▴ 790
8
votes
9
replies
747
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 3 months ago by
Hervé Pagès
15k • written 4 months ago by
jon.klonowski
▴ 30
8
votes
8
replies
1.7k
views
biomaRt: drerio_gene_ensembl dataset missing
biomart
ensembl
ripseeker
updated 4.5 years ago by
Mike Smith
★ 5.5k • written 4.5 years ago by
António Miguel de Jesus Domingues
▴ 480
6
votes
5
replies
2.6k
views
biomaRt Ensembl gene ID to multiple HGNC symbol
ensembl
symbol
hgnc
biomart
updated 3.0 years ago by
James W. MacDonald
59k • written 3.0 years ago by
foehn
▴ 80
6
votes
5
replies
7.1k
views
biomaRt: no access to Ensembl_75 (GRCh37.p13)
biomarRt
ensembl
updated 7.5 years ago by
springbreeze.autumncolor
• 0 • written 7.6 years ago by
Jennifer Becq
• 0
6
votes
11
replies
1.7k
views
ensembldb from M.musculus NCBI37 v67 gtf
ensembldb
NCBI37
v67
ensembl
4.3 years ago
floriandeckert
▴ 30
5
votes
12
replies
1.3k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 9 days ago by
Johannes Rainer
★ 1.9k • written 3.5 years ago by
Guido Hooiveld
★ 3.2k
5
votes
5
replies
1.3k
views
News:
Ensembl 88 is out!
ensembl
ensembl mart
biomart
e!88
News
5.2 years ago
Thomas Maurel
▴ 790
5
votes
2
replies
1.8k
views
News:
Ensembl release 81 is out!
human
mouse
GRCh38
biomart
Ensembl
News
updated 6.9 years ago by
Sonali Arora
▴ 380 • written 6.9 years ago by
Thomas Maurel
▴ 790
4
votes
5
replies
769
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 3.1 years ago by
James W. MacDonald
59k • written 3.1 years ago by
kushshah
▴ 10
4
votes
9
replies
2.0k
views
News:
Ensembl release 84 is out!
ensembl
mart
release84
biomart
ensembl release
News
updated 6.1 years ago by
arielpaulson
▴ 20 • written 6.2 years ago by
Thomas Maurel
▴ 790
4
votes
17
replies
1.0k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt
annotation
Ensembl
annotationHub
updated 21 months ago by
Kevin Blighe
3.5k • written 21 months ago by
Didi
▴ 10
4
votes
4
replies
556
views
biomaRt getSequence fails with genomic coordinates
biomart
getSequence
genomic coordinates
ENSEMBL
bug report
updated 2.3 years ago by
Mike Smith
★ 5.5k • written 2.3 years ago by
Ni-Ar
▴ 10
4
votes
5
replies
1.2k
views
ChIPpeakAnno getAnnotation request fail
chippeakanno
biomart
ensembl
6.4 years ago
igor
▴ 40
4
votes
11
replies
654
views
Dealing with duplicated genes in camera gene set testing
limma
camera
gene set testing
ensembl
updated 2.4 years ago by
Robert Castelo
★ 2.9k • written 2.4 years ago by
Jeremy Beales
▴ 10
4
votes
8
replies
6.7k
views
Ensembl site unresponsive
ensembl
biomart
updated 13 months ago by
tommaso.gastaldi
• 0 • written 19 months ago by
lirongrossmann
▴ 40
4
votes
1
reply
4.7k
views
Finding orthologous human/mouse ENSEMBL IDs
human
mouse
ensembl
annotationdbi
homologue
5.0 years ago • updated 4.9 years ago
Keith Hughitt
▴ 150
3
votes
6
replies
1.2k
views
biomaRt: Ensembl -> Entrez conversion error?
biomart
entrez gene identifiers
ensembl
conversion
updated 3.5 years ago by
Mike Smith
★ 5.5k • written 3.5 years ago by
EdgeR_A_Poe
▴ 10
3
votes
6
replies
1.2k
views
Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
annotation
ensembl
annotationdbi
3.9 years ago
vd4mmind
• 0
3
votes
14
replies
2.7k
views
biomaRt - Error in getBM: The query to the BioMart webservice returned an invalid result
biomart
error
ensembl
bioconductor
ensembl mart
5.0 years ago
daniel.carbajo
• 0
3
votes
2
replies
540
views
GEO Download - "The query to BioMart webservice returned an invalid result..."
biomart
geo
software error
ensembl
updated 3.0 years ago by
Mike Smith
★ 5.5k • written 3.0 years ago by
wes
▴ 10
2
votes
0
replies
416
views
News:
ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
updated 3.0 years ago by
nguyenlieuduoc
• 0 • written 3.1 years ago by
shepherl
3.1k
2
votes
3
replies
8.9k
views
BiomaRt: protein coding transcript identification
ensembl
protein coding
biomart
updated 7.6 years ago by
Thomas Maurel
▴ 790 • written 7.6 years ago by
Brian Smith
▴ 120
2
votes
2
replies
838
views
goseq package: Is the package in sync with the most current Ensembl release?
goseq
ensembl
updated 6.1 years ago by
Johannes Rainer
★ 1.9k • written 6.1 years ago by
mrodrigues.fernanda
▴ 10
2
votes
1
reply
847
views
Why does biomaRt query show inconsistent behavior with ensembl versions from March and May
biomart
ensembl
6.9 years ago
jmeisig
▴ 20
2
votes
3
replies
618
views
make TxDb from list of genes
R
maketxdbfrombiomart
maketxdbfromgranges
rstudio
ensembl
3.5 years ago
rtwest
• 0
2
votes
1
reply
841
views
GoSeq: use ENSEMBLTRANS as input
goseq
ensembl
updated 7.0 years ago by
Nadia Davidson
▴ 310 • written 7.0 years ago by
idomtamir
▴ 10
2
votes
1
reply
829
views
News:
Ensembl 91 is out!
ensembl
biomart
release
ensembl91
News
4.5 years ago
amonida
▴ 20
2
votes
1
reply
1.0k
views
Ensemble and Entrez disconnected?
ensembl
entrez
biomart
org.hs.eg.db
updated 3.5 years ago by
James W. MacDonald
59k • written 3.5 years ago by
bettina.budeus
• 0
2
votes
3
replies
215
views
Ensembl non responsive
ensembl
R
6 weeks ago
ksci
▴ 10
2
votes
2
replies
1.3k
views
BioMart missing IDs
biomart
ensembl
entrez gene identifiers
updated 3.8 years ago by
James W. MacDonald
59k • written 3.8 years ago by
rina
▴ 20
2
votes
3
replies
243
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
24 days ago • updated 16 days ago
kieran.short
▴ 10
2
votes
1
reply
127
views
Can Rsubread output use Ensembl gene IDs
Ensembl
Rsubread
updated 8 weeks ago by
Gordon Smyth
45k • written 8 weeks ago by
agustin.gonvi
▴ 10
2
votes
2
replies
517
views
Ensembl sheep dataset in biomaRt
ensembl
biomart
oaries
updated 3.8 years ago by
Mike Smith
★ 5.5k • written 3.8 years ago by
pokharel.kisun
• 0
2
votes
0
replies
96
views
News:
News:Ensembl 106 has just been released!
ensembl
biomaRt
ensembldb
6 weeks ago
Benjamin
▴ 20
2
votes
12
replies
1.9k
views
biomaRt does not return entrezgene id
bioconductor
biomart
entrez gene identifiers
ensembl
ensembl mart
updated 5.1 years ago by
Thomas Maurel
▴ 790 • written 5.1 years ago by
daniel.carbajo
• 0
2
votes
11
replies
3.1k
views
biomaRT connexion problem make failed my unit tests
biomaRt
Peer's Certificate
Ensembl
updated 16 months ago by
Mike Smith
★ 5.5k • written 20 months ago by
ilysR
• 0
2
votes
6
replies
1.2k
views
biomaRt Ensembl ID query returns NA in 'ensembl_gene_id', 'ensembl_transcript_id', etc.
biomart
ensembl
annotation
updated 4.9 years ago by
Mike Smith
★ 5.5k • written 4.9 years ago by
yura.grabovska
▴ 30
2
votes
4
replies
1.1k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl
macaque
dbsnp
customprodb
updated 6.9 years ago by
xiaojing.wang
▴ 50 • written 6.9 years ago by
kristenbeck527
• 0
2
votes
2
replies
886
views
BiomaRt returns 0 obs
biomart
getbm
ensembl
updated 3.8 years ago by
James W. MacDonald
59k • written 3.8 years ago by
edelman
• 0
2
votes
3
replies
757
views
Problem for finding "Locus Link ID" from Annotation file
wgcna package
TCGA
LocusLinkID
genecode
ensembl
updated 3.6 years ago by
James W. MacDonald
59k • written 3.6 years ago by
modarzi
▴ 10
1
vote
5
replies
1.8k
views
Ensembl bacteria not accessible from biomaRt
biomart
ensembl
updated 6.0 years ago by
Martin Morgan
25k • written 6.0 years ago by
arielpaulson
▴ 20
1
vote
2
replies
788
views
get_gene_transcript_exon_tables.pl extremely slow
ensembl
ensembldb
updated 4.6 years ago by
Johannes Rainer
★ 1.9k • written 4.6 years ago by
Ed Siefker
▴ 230
1
vote
0
replies
948
views
News:
ensembl 90 ensembldb EnsDb databases have been added to AnnotationHub
ensemblb
ensembl
AnnotationHub
annotation
News
4.7 years ago
Johannes Rainer
★ 1.9k
1
vote
2
replies
2.5k
views
Converting annotation from UCSC to Ensembl
ensembl
ucsc
annotation
updated 6.5 years ago by
James W. MacDonald
59k • written 6.5 years ago by
AB
▴ 100
1
vote
1
reply
888
views
News:
Ensembl 90 has been released
ensembl
biomart
ensembl90
release
News
4.8 years ago
Thomas Maurel
▴ 790
50 results • Page
1 of 1
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Comment: Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
by
Lan Anh
• 0
Hello, Sorry for the late answer, I called several packages after my error and I do not know how it worked after that. Thank you for the h…
Comment: LogFC values in edgeR - w/wo intercept
by
JK Kim
• 0
Thanks, Dr. Smyth!
Comment: LogFC values in edgeR - w/wo intercept
by
JK Kim
• 0
Oops. I just corrected the URL. Thank you Dr. Smyth.
Comment: Fail to run RupRadar
by
Qingwei
• 0
Dear Sergi, Yeah, it works. ```r dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads, GTF.featureType="cDNA_match", GTF.attrType="ID…
Comment: LogFC values in edgeR - w/wo intercept
by
Gordon Smyth
45k
The link you've entered for "A guide to creating design matrices for gene expression experiments" doesn't work. Could you please correct th…
Votes
Comment: LogFC values in edgeR - w/wo intercept
Answer: LogFC values in edgeR - w/wo intercept
Answer: LogFC values in edgeR - w/wo intercept
Answer: broken chain import in liftOver
Answer: toGRanges help!
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