Showing : Ensembl • reset
16
votes
7
replies
10k
views
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2 ensembl
updated 5.7 years ago by 63k • written 5.7 years ago by ▴ 150
15
votes
13
replies
2.3k
views
celldex ensembl gene annotation issue
SingleR celldex HumanPrimaryCellAtlasData ensembl
updated 23 months ago by ▴ 10 • written 23 months ago by ▴ 20
13
votes
8
replies
15k
views
how to use biomaRt with ensembl build 37
biomaRt ensembl GRCh37
updated 9.0 years ago by ▴ 800 • written 9.0 years ago by ▴ 90
10
votes
8
replies
2.2k
views
Best alternative annotation package to BiomaRt
R biomaRt Ensembl rnaseq
4.3 years ago m93 ▴ 10
9
votes
1
reply
2.0k
views
News: Ensembl release 80 is out!
biomart Ensembl zebrafish Rat 1000 genomes phase 3 News
updated 8.4 years ago by ▴ 390 • written 8.4 years ago by ▴ 800
8
votes
9
replies
4.1k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 20 months ago by 16k • written 20 months ago by ▴ 40
8
votes
8
replies
2.4k
views
biomaRt: drerio_gene_ensembl dataset missing
biomart ensembl ripseeker
updated 5.8 years ago by ★ 6.1k • written 5.8 years ago by ▴ 490
7
votes
25
replies
3.6k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 25 days ago by • 0 • written 4.9 years ago by ★ 3.7k
7
votes
4
replies
4.8k
views
biomaRt server error, and mirrors do not help
ensembl biomaRt R
updated 10 months ago by ▴ 10 • written 17 months ago by ▴ 40
6
votes
5
replies
4.4k
views
biomaRt Ensembl gene ID to multiple HGNC symbol
ensembl symbol hgnc biomart
updated 4.4 years ago by 63k • written 4.4 years ago by ▴ 80
6
votes
11
replies
2.8k
views
ensembldb from M.musculus NCBI37 v67 gtf
ensembldb NCBI37 v67 ensembl
5.7 years ago • updated 5.6 years ago floriandeckert ▴ 30
6
votes
1
reply
5.8k
views
Finding orthologous human/mouse ENSEMBL IDs
human mouse ensembl annotationdbi homologue
6.3 years ago Keith Hughitt ▴ 180
6
votes
5
replies
7.8k
views
biomaRt: no access to Ensembl_75 (GRCh37.p13)
biomarRt ensembl
updated 8.9 years ago by • 0 • written 8.9 years ago by • 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
5
votes
5
replies
1.8k
views
News: Ensembl 88 is out!
ensembl ensembl mart biomart e!88 News
6.5 years ago Thomas Maurel ▴ 800
5
votes
2
replies
2.4k
views
News: Ensembl release 81 is out!
human mouse GRCh38 biomart Ensembl News
updated 8.2 years ago by ▴ 390 • written 8.2 years ago by ▴ 800
4
votes
5
replies
1.2k
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 4.5 years ago by 63k • written 4.5 years ago by ▴ 10
4
votes
9
replies
2.6k
views
News: Ensembl release 84 is out!
ensembl mart release84 biomart ensembl release News
updated 7.5 years ago by ▴ 20 • written 7.6 years ago by ▴ 800
4
votes
5
replies
1.5k
views
ChIPpeakAnno getAnnotation request fail
chippeakanno biomart ensembl
7.7 years ago igor ▴ 40
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 3.8k • written 3.1 years ago by ▴ 10
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 ★ 6.1k • written 3.6 years ago by ▴ 10
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 ★ 3.0k • written 3.8 years ago by ▴ 10
4
votes
8
replies
12k
views
Ensembl site unresponsive
ensembl biomart
updated 2.5 years ago by • 0 • written 3.0 years ago by ▴ 40
3
votes
6
replies
1.7k
views
biomaRt: Ensembl -> Entrez conversion error?
biomart entrez gene identifiers ensembl conversion
updated 4.9 years ago by ★ 6.1k • written 4.9 years ago by ▴ 10
3
votes
6
replies
2.4k
views
Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
annotation ensembl annotationdbi
5.3 years ago vd4mmind • 0
3
votes
14
replies
3.3k
views
biomaRt - Error in getBM: The query to the BioMart webservice returned an invalid result
biomart error ensembl bioconductor ensembl mart
6.3 years ago daniel.carbajo • 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 ★ 6.1k • written 4.3 years ago by ▴ 10
2
votes
1
reply
1.0k
views
Why does biomaRt query show inconsistent behavior with ensembl versions from March and May
biomart ensembl
8.3 years ago jmeisig ▴ 20
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 • 0 • written 4.4 years ago by 3.5k
2
votes
3
replies
10k
views
BiomaRt: protein coding transcript identification
ensembl protein coding biomart
updated 8.9 years ago by ▴ 800 • written 8.9 years ago by ▴ 120
2
votes
2
replies
1.1k
views
goseq package: Is the package in sync with the most current Ensembl release?
goseq ensembl
updated 7.5 years ago by ★ 2.0k • written 7.5 years ago by ▴ 10
2
votes
4
replies
1.3k
views
make TxDb from list of genes
R maketxdbfrombiomart maketxdbfromgranges rstudio ensembl
updated 5 months ago by • 0 • written 4.8 years ago by • 0
2
votes
1
reply
1.1k
views
GoSeq: use ENSEMBLTRANS as input
goseq ensembl
updated 8.4 years ago by ▴ 310 • written 8.4 years ago by ▴ 10
2
votes
1
reply
1.1k
views
News: Ensembl 91 is out!
ensembl biomart release ensembl91 News
5.8 years ago amonida ▴ 20
2
votes
1
reply
1.5k
views
Ensemble and Entrez disconnected?
ensembl entrez biomart org.hs.eg.db
updated 4.8 years ago by 63k • written 4.8 years ago by • 0
2
votes
3
replies
986
views
Ensembl non responsive
ensembl R
18 months ago ksci ▴ 20
2
votes
2
replies
1.3k
views
BiomaRt returns 0 obs
biomart getbm ensembl
updated 5.1 years ago by 63k • written 5.1 years ago by • 0
2
votes
2
replies
2.0k
views
BioMart missing IDs
biomart ensembl entrez gene identifiers
updated 5.2 years ago by 63k • written 5.2 years ago by ▴ 20
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 6.2 years ago by ★ 6.1k • written 6.2 years ago by ▴ 30
2
votes
1
reply
753
views
Can Rsubread output use Ensembl gene IDs
Ensembl Rsubread
updated 18 months ago by 48k • written 18 months ago by ▴ 20
2
votes
2
replies
805
views
Ensembl sheep dataset in biomaRt
ensembl biomart oaries
updated 5.1 years ago by ★ 6.1k • written 5.1 years ago by • 0
2
votes
0
replies
523
views
News: News:Ensembl 106 has just been released!
ensembl biomaRt ensembldb
17 months ago Benjamin ▴ 20
2
votes
12
replies
2.5k
views
biomaRt does not return entrezgene id
bioconductor biomart entrez gene identifiers ensembl ensembl mart
updated 6.5 years ago by ▴ 800 • written 6.5 years ago by • 0
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 ★ 6.1k • written 3.0 years ago by • 0
2
votes
4
replies
1.5k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl macaque dbsnp customprodb
updated 8.2 years ago by ▴ 50 • written 8.2 years ago by • 0
2
votes
3
replies
1.2k
views
Problem for finding "Locus Link ID" from Annotation file
wgcna package TCGA LocusLinkID genecode ensembl
updated 5.0 years ago by 63k • written 5.0 years ago by ▴ 10
1
vote
5
replies
2.5k
views
Ensembl bacteria not accessible from biomaRt
biomart ensembl
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 20
1
vote
2
replies
1.1k
views
get_gene_transcript_exon_tables.pl extremely slow
ensembl ensembldb
updated 5.9 years ago by ★ 2.0k • written 5.9 years ago by ▴ 230
1
vote
0
replies
1.2k
views
News: ensembl 90 ensembldb EnsDb databases have been added to AnnotationHub
ensemblb ensembl AnnotationHub annotation News
6.1 years ago Johannes Rainer ★ 2.0k
1
vote
2
replies
3.2k
views
Converting annotation from UCSC to Ensembl
ensembl ucsc annotation
updated 7.8 years ago by 63k • written 7.8 years ago by ▴ 110
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
Awards • All
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