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13
votes
8
replies
15k
views
how to use biomaRt with ensembl build 37
biomaRt ensembl GRCh37
updated 9.1 years ago by ▴ 800 • written 9.1 years ago by ▴ 90
4
votes
8
replies
12k
views
Ensembl site unresponsive
ensembl biomart
updated 2.6 years ago by • 0 • written 3.1 years ago by ▴ 40
17
votes
7
replies
11k
views
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2 ensembl
updated 5.8 years ago by 64k • written 5.8 years ago by ▴ 150
2
votes
3
replies
10k
views
BiomaRt: protein coding transcript identification
ensembl protein coding biomart
updated 9.1 years ago by ▴ 800 • written 9.1 years ago by ▴ 120
6
votes
5
replies
7.9k
views
biomaRt: no access to Ensembl_75 (GRCh37.p13)
biomarRt ensembl
updated 9.1 years ago by • 0 • written 9.1 years ago by • 0
6
votes
1
reply
5.9k
views
Finding orthologous human/mouse ENSEMBL IDs
human mouse ensembl annotationdbi homologue
6.5 years ago Keith Hughitt ▴ 180
7
votes
5
replies
5.4k
views
biomaRt server error, and mirrors do not help
ensembl biomaRt R
updated 7 weeks ago by • 0 • written 19 months ago by ▴ 40
2
votes
11
replies
5.3k
views
biomaRT connexion problem make failed my unit tests
biomaRt Peer's Certificate Ensembl
updated 2.8 years ago by ★ 6.2k • written 3.2 years ago by • 0
8
votes
5
replies
4.7k
views
biomaRt Ensembl gene ID to multiple HGNC symbol
ensembl symbol hgnc biomart
updated 4.6 years ago by 64k • written 4.6 years ago by ▴ 100
8
votes
9
replies
4.5k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 22 months ago by 16k • written 22 months ago by ▴ 40
0
votes
5
replies
4.3k
views
Ensembl biomaRt connection errors
software error biomart ensembl
updated 7.5 years ago by ▴ 70 • written 7.5 years ago by • 0
7
votes
26
replies
4.1k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 6 weeks ago by • 0 • written 5.0 years ago by ★ 3.8k
1
vote
4
replies
3.5k
views
ensembl not working...?
ensembl biomart
5.6 years ago JoeMG • 0
3
votes
14
replies
3.4k
views
biomaRt - Error in getBM: The query to the BioMart webservice returned an invalid result
biomart error ensembl bioconductor ensembl mart
6.5 years ago daniel.carbajo • 0
1
vote
2
replies
3.2k
views
Converting annotation from UCSC to Ensembl
ensembl ucsc annotation
updated 8.0 years ago by 64k • written 8.0 years ago by ▴ 110
6
votes
11
replies
2.9k
views
ensembldb from M.musculus NCBI37 v67 gtf
ensembldb NCBI37 v67 ensembl
5.8 years ago floriandeckert ▴ 30
4
votes
9
replies
2.7k
views
News: Ensembl release 84 is out!
ensembl mart release84 biomart ensembl release News
updated 7.6 years ago by ▴ 20 • written 7.7 years ago by ▴ 800
2
votes
12
replies
2.6k
views
biomaRt does not return entrezgene id
bioconductor biomart entrez gene identifiers ensembl ensembl mart
updated 6.7 years ago by ▴ 800 • written 6.7 years ago by • 0
1
vote
5
replies
2.6k
views
Ensembl bacteria not accessible from biomaRt
biomart ensembl
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 20
8
votes
8
replies
2.6k
views
biomaRt: drerio_gene_ensembl dataset missing
biomart ensembl ripseeker
updated 6.0 years ago by ★ 6.2k • written 6.0 years ago by ▴ 490
15
votes
13
replies
2.6k
views
celldex ensembl gene annotation issue
SingleR celldex HumanPrimaryCellAtlasData ensembl
updated 2.1 years ago by ▴ 10 • written 2.1 years ago by ▴ 20
3
votes
6
replies
2.5k
views
Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
annotation ensembl annotationdbi
5.5 years ago vd4mmind • 0
5
votes
2
replies
2.5k
views
News: Ensembl release 81 is out!
human mouse GRCh38 biomart Ensembl News
updated 8.4 years ago by ▴ 390 • written 8.4 years ago by ▴ 800
2
votes
1
reply
2.4k
views
biomaRt: list of hosts accessed
biomart ensembl
updated 6.4 years ago by ★ 6.2k • written 6.4 years ago by ▴ 10
0
votes
5
replies
2.4k
views
getBM in loop
biomart ensembl curl
updated 5.9 years ago by ★ 6.2k • written 5.9 years ago by ▴ 40
10
votes
8
replies
2.4k
views
Best alternative annotation package to BiomaRt
R biomaRt Ensembl rnaseq
4.4 years ago m93 ▴ 10
0
votes
7
replies
2.3k
views
BioMart does not find mouse homologs of human genes
biomart homolog ortholog gene conversion ensembl
updated 4.2 years ago by 64k • written 4.2 years ago by ▴ 30
0
votes
3
replies
2.2k
views
biomaRt fails for M.musculus annotation, Ensembl version 80
biomart ensembl
updated 8.2 years ago by ▴ 20 • written 8.2 years ago by ▴ 80
1
vote
3
replies
2.2k
views
Convert mouse gene ids to hamster gene ids
biomart R ensembl
updated 9 months ago by 3.9k • written 3.4 years ago by • 0
4
votes
17
replies
2.1k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 3.3 years ago by 3.9k • written 3.3 years ago by ▴ 10
2
votes
2
replies
2.1k
views
BioMart missing IDs
biomart ensembl entrez gene identifiers
updated 5.3 years ago by 64k • written 5.3 years ago by ▴ 30
9
votes
1
reply
2.1k
views
News: Ensembl release 80 is out!
biomart Ensembl zebrafish Rat 1000 genomes phase 3 News
updated 8.5 years ago by ▴ 390 • written 8.5 years ago by ▴ 800
0
votes
6
replies
2.1k
views
converting UniProt to SGD ids using UniProt.wd
uniprot.ws uniprot ensembl
updated 8.9 years ago by ★ 7.2k • written 8.9 years ago by ▴ 160
1
vote
3
replies
2.0k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub Ensembl Mouse AnnotationHub Ensembl
4.0 years ago dmgatti ▴ 10
0
votes
2
replies
2.0k
views
use BiomartGeneRegionTrack with the dataset grch37.ensembl.org
gviz ensembl biomart
9.0 years ago Tiphaine Martin ▴ 40
5
votes
5
replies
1.9k
views
News: Ensembl 88 is out!
ensembl ensembl mart biomart e!88 News
6.7 years ago Thomas Maurel ▴ 800
2
votes
6
replies
1.8k
views
biomaRt Ensembl ID query returns NA in 'ensembl_gene_id', 'ensembl_transcript_id', etc.
biomart ensembl annotation
updated 6.4 years ago by ★ 6.2k • written 6.4 years ago by ▴ 30
3
votes
6
replies
1.8k
views
biomaRt: Ensembl -> Entrez conversion error?
biomart entrez gene identifiers ensembl conversion
updated 5.0 years ago by ★ 6.2k • written 5.0 years ago by ▴ 10
0
votes
4
replies
1.7k
views
biomaRT getBM error
biomart getbm ensembl
updated 5.8 years ago by ★ 6.2k • written 5.8 years ago by • 0
0
votes
3
replies
1.7k
views
How to produce a dataframe with unique ENTREZID to use in gage?
gage annotationdbi entrez ensembl
5.8 years ago colaneri ▴ 30
0
votes
2
replies
1.7k
views
Gviz - adding ensembl gene annotation track
gviz ensembl
7.3 years ago just • 0
0
votes
2
replies
1.7k
views
Error in martCheck(mart, c("ensembl", "ENSEMBL_MART_ENSEMBL")) : No dataset selected, please select a dataset first.
biomart mart ensembl
updated 3.7 years ago by 64k • written 3.7 years ago by • 0
0
votes
3
replies
1.6k
views
DESeq2: removal of duplicated genes during statistical analysis
deseq2 gene symbol ensembl
updated 5.0 years ago by 41k • written 5.0 years ago by ▴ 10
4
votes
11
replies
1.6k
views
Dealing with duplicated genes in camera gene set testing
limma camera gene set testing ensembl
updated 4.0 years ago by ★ 3.0k • written 4.0 years ago by ▴ 10
0
votes
5
replies
1.6k
views
News: Ensembl 79 release is out!
Ensembl biomart release news News
updated 8.7 years ago by ★ 8.2k • written 8.7 years ago by ▴ 20
4
votes
5
replies
1.6k
views
ChIPpeakAnno getAnnotation request fail
chippeakanno biomart ensembl
7.9 years ago igor ▴ 40
2
votes
4
replies
1.5k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl macaque dbsnp customprodb
updated 8.4 years ago by ▴ 50 • written 8.4 years ago by • 0
0
votes
1
reply
1.5k
views
Problem with visualising empty tracks from ensembl
gviz ensembl
updated 8.3 years ago by ★ 1.6k • written 8.3 years ago by • 0
2
votes
1
reply
1.5k
views
Ensemble and Entrez disconnected?
ensembl entrez biomart org.hs.eg.db
updated 5.0 years ago by 64k • written 5.0 years ago by • 0
0
votes
0
replies
1.5k
views
News: Ensembl 83 is out!
ensemble mart ensembl biomart ensembl release News
8.0 years ago amonida ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl down??? by James W. MacDonald 64k
I normally caution against mapping between annotation sources (NCBI and Ensembl), as it usually doesn't work well. However, it is possible.…
Answer: NCBI protein conversion to CDNA and NCBI gene (in R) by James W. MacDonald 64k
I already showed you how to do this for gene symbols, and it's analogous for any other annotation ID. Please see the `AnnotationDbi` [vigne…
Comment: Obtaining rsIDs with ENSG and variant ID information by Robert Castelo ★ 3.0k
This is a large package, and when downloading and installing large packages it's often the case to get timeouts. Try setting a longer time …
Comment: How does Deseq2 deal with the row with zero when calculating size factors by ATpoint ★ 3.6k
> Because I found that if there is at least one gene without zero among all of the samples, the deseq2 runs smoothly. No, it doesn't. ``…
Comment: Obtaining rsIDs with ENSG and variant ID information by bd2000 • 0
Thank you for your answer. I've tried to download the package but it didn't work: Error in download.file(url, destfile, method, mode =…
Votes
Answer: biomaRt not working - lazy table error
Answer: Confused about the CPM and TMM normalization in edgeR
Answer: Differential gene expression analysis
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
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