Showing : Ensembl • reset
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
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
0
votes
6
replies
2.0k
views
converting UniProt to SGD ids using UniProt.wd
uniprot.ws uniprot ensembl
updated 8.7 years ago by ★ 7.2k • written 8.7 years ago by ▴ 160
0
votes
3
replies
2.1k
views
biomaRt fails for M.musculus annotation, Ensembl version 80
biomart ensembl
updated 8.1 years ago by ▴ 20 • written 8.1 years ago by ▴ 80
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
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
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
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
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
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
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
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
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
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
1
vote
2
replies
975
views
Using Ensmbl rel 80, when rel 79 is supported by BioConductor
ensembl
updated 8.2 years ago by ★ 2.0k • written 8.2 years ago by • 0
0
votes
6
replies
1.2k
views
How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq methylation ensembl ucsc limma
5.6 years ago dusan.petrovic • 0
0
votes
6
replies
1.2k
views
ENSEMBL causing issues replicating previous results
R ENSEMBL topGO
5.8 years ago snguyen268 • 0
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
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
0
votes
2
replies
2.0k
views
use BiomartGeneRegionTrack with the dataset grch37.ensembl.org
gviz ensembl biomart
8.8 years ago Tiphaine Martin ▴ 40
0
votes
3
replies
1.6k
views
How to produce a dataframe with unique ENTREZID to use in gage?
gage annotationdbi entrez ensembl
5.6 years ago colaneri ▴ 30
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
0
votes
6
replies
1.4k
views
Getting paralogus genes from biomart for mouse
biomart biomaRt Ensembl
updated 2.2 years ago by 3.8k • written 2.2 years ago by • 0
0
votes
2
replies
1.6k
views
Gviz - adding ensembl gene annotation track
gviz ensembl
7.1 years ago just • 0
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
0
votes
5
replies
2.4k
views
getBM in loop
biomart ensembl curl
updated 5.8 years ago by ★ 6.1k • written 5.8 years ago by ▴ 40
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
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
0
votes
5
replies
4.2k
views
Ensembl biomaRt connection errors
software error biomart ensembl
updated 7.3 years ago by ▴ 70 • written 7.3 years ago by • 0
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
0
votes
2
replies
1.4k
views
Ensembl database query with biomart behaves strangely when using chromosomes as filter values
biomart ensembl
updated 8.3 years ago by ▴ 800 • written 8.3 years ago by ▴ 20
0
votes
1
reply
783
views
Ensembl version from non-vertebrate biomaRt
biomart ensembl
updated 7.4 years ago by ▴ 70 • written 7.4 years ago by ▴ 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
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
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
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
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
1
vote
1
reply
961
views
biomaRt getBM() function does not recognize gene ID character vector values generated from csv file for annotation
biomart getBM() csv files annotation ensembl
updated 5.2 years ago by ★ 6.1k • written 5.2 years ago by ▴ 10
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
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
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
0
votes
1
reply
954
views
how to set boolean filter
biomart ensembl boolean filter
5.7 years ago shenwei1376 • 0
0
votes
1
reply
2.2k
views
biomaRt: list of hosts accessed
biomart ensembl
updated 6.2 years ago by ★ 6.1k • written 6.2 years ago by • 0
0
votes
1
reply
1.3k
views
Scan issue retrieving Drosophila Genes with biomaRt
R biomart drosophila melanogaster ensembl
updated 5.6 years ago by ★ 6.1k • written 5.6 years ago by • 0
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
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
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
0
votes
4
replies
1.6k
views
biomaRT getBM error
biomart getbm ensembl
updated 5.6 years ago by ★ 6.1k • written 5.6 years ago by • 0
0
votes
3
replies
910
views
DESeq2 output with multiple Ensembl Gene Names per row, how to resolve?
rnaseq deseq2 ensembl
updated 6.4 years ago by 40k • written 6.4 years ago by • 0
0
votes
1
reply
1.5k
views
Problem with visualising empty tracks from ensembl
gviz ensembl
updated 8.1 years ago by ★ 1.6k • written 8.1 years ago by • 0
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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