Showing : Ensembl • reset
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
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
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
0
votes
14
replies
1.2k
views
Error while opening Mart with biomaRt package
software error ensembl biomart
3.8 years ago loicborcard01 • 0
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
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
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
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
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
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
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
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
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
7
replies
2.1k
views
BioMart does not find mouse homologs of human genes
biomart homolog ortholog gene conversion ensembl
updated 4.0 years ago by 63k • written 4.0 years ago by ▴ 30
1
vote
7
replies
877
views
News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
5.0 years ago shepherl 3.5k
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
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
714
views
Anyone else having trouble with biomaRt (Oct 10, 2019)
ensembl biomaRt
updated 4.0 years ago by ★ 6.1k • written 4.0 years ago by ★ 1.3k
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
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
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
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
0
votes
6
replies
1.2k
views
ENSEMBL causing issues replicating previous results
R ENSEMBL topGO
5.8 years ago snguyen268 • 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
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
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
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
4
votes
5
replies
1.5k
views
ChIPpeakAnno getAnnotation request fail
chippeakanno biomart ensembl
7.7 years ago igor ▴ 40
0
votes
5
replies
1.5k
views
News: Ensembl 79 release is out!
Ensembl biomart release news News
updated 8.6 years ago by ★ 8.2k • written 8.6 years ago by ▴ 20
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
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
0
votes
5
replies
1.3k
views
Using mgeneSim with Ensembl ids
Ensembl GOsemsim GO semantic similarity
updated 7.1 years ago by ★ 1.2k • written 7.1 years ago by ▴ 10
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
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
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
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
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
4
replies
1.1k
views
Error message: "Request to BioMart web service failed."
BiocManager biomaRt listMarts() ensembl Biomart
updated 4.3 years ago by ★ 6.1k • written 4.3 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
1
vote
4
replies
3.4k
views
ensembl not working...?
ensembl biomart
5.4 years ago JoeMG • 0
0
votes
4
replies
835
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 3.5 years ago by 40k • written 3.5 years ago by • 0
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
1
vote
3
replies
2.0k
views
Convert mouse gene ids to hamster gene ids
biomart R ensembl
updated 7 months ago by 3.8k • written 3.2 years ago by • 0
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
0
votes
3
replies
1.6k
views
DESeq2: removal of duplicated genes during statistical analysis
deseq2 gene symbol ensembl
updated 4.9 years ago by 40k • written 4.9 years ago by ▴ 10
1
vote
3
replies
1.9k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub Ensembl Mouse AnnotationHub Ensembl
3.8 years ago dmgatti ▴ 10
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
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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Popular Question to Gordon Smyth 48k
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Popular Question to James W. MacDonald 63k
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