Showing : ensembl • reset
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 13 days ago by • 0 • written 5.4 years ago by ★ 3.9k
4
votes
17
replies
2.4k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt annotation Ensembl annotationHub
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by ▴ 10
3
votes
14
replies
3.6k
views
biomaRt - Error in getBM: The query to the BioMart webservice returned an invalid result
biomart error ensembl bioconductor ensembl mart
6.9 years ago daniel.carbajo • 0
0
votes
14
replies
1.7k
views
Error while opening Mart with biomaRt package
software error ensembl biomart
4.4 years ago loicborcard01 • 0
15
votes
13
replies
3.0k
views
celldex ensembl gene annotation issue
SingleR celldex HumanPrimaryCellAtlasData ensembl
updated 2.4 years ago by ▴ 10 • written 2.4 years ago by ▴ 20
2
votes
12
replies
2.9k
views
biomaRt does not return entrezgene id
bioconductor biomart entrez gene identifiers ensembl ensembl mart
updated 7.0 years ago by ▴ 800 • written 7.0 years ago by • 0
4
votes
11
replies
1.9k
views
Dealing with duplicated genes in camera gene set testing
limma camera gene set testing ensembl
updated 4.3 years ago by ★ 3.2k • written 4.3 years ago by ▴ 10
6
votes
11
replies
3.2k
views
ensembldb from M.musculus NCBI37 v67 gtf
ensembldb NCBI37 v67 ensembl
6.2 years ago floriandeckert ▴ 30
9
votes
11
replies
5.6k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 5 weeks ago by 3.8k • written 2.2 years ago by ▴ 40
2
votes
11
replies
6.0k
views
biomaRT connexion problem make failed my unit tests
biomaRt Peer's Certificate Ensembl
updated 3.2 years ago by ★ 6.5k • written 3.6 years ago by • 0
4
votes
9
replies
2.9k
views
News: Ensembl release 84 is out!
ensembl mart release84 biomart ensembl release News
updated 8.0 years ago by ▴ 20 • written 8.1 years ago by ▴ 800
8
votes
8
replies
2.8k
views
biomaRt: drerio_gene_ensembl dataset missing
biomart ensembl ripseeker
updated 6.4 years ago by ★ 6.5k • written 6.4 years ago by ▴ 490
13
votes
8
replies
16k
views
how to use biomaRt with ensembl build 37
biomaRt ensembl GRCh37
updated 9.5 years ago by ▴ 800 • written 9.5 years ago by ▴ 90
10
votes
8
replies
2.9k
views
Best alternative annotation package to BiomaRt
R biomaRt Ensembl rnaseq
4.8 years ago m93 ▴ 10
5
votes
8
replies
14k
views
Ensembl site unresponsive
ensembl biomart
updated 3.0 years ago by • 0 • written 3.5 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 6.2 years ago by 65k • written 6.2 years ago by ▴ 150
0
votes
7
replies
2.7k
views
BioMart does not find mouse homologs of human genes
biomart homolog ortholog gene conversion ensembl
updated 4.5 years ago by 65k • written 4.5 years ago by ▴ 30
1
vote
7
replies
1.1k
views
News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
5.5 years ago shepherl 3.8k
3
votes
6
replies
2.0k
views
biomaRt: Ensembl -> Entrez conversion error?
biomart entrez gene identifiers ensembl conversion
updated 5.4 years ago by ★ 6.5k • written 5.4 years ago by ▴ 10
0
votes
6
replies
1.4k
views
How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq methylation ensembl ucsc limma
6.2 years ago • updated 6.1 years ago dusan.petrovic • 0
0
votes
6
replies
937
views
Anyone else having trouble with biomaRt (Oct 10, 2019)
ensembl biomaRt
updated 4.5 years ago by ★ 6.5k • written 4.5 years ago by ★ 1.3k
0
votes
6
replies
1.7k
views
Getting paralogus genes from biomart for mouse
biomart biomaRt Ensembl
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
0
votes
6
replies
2.3k
views
converting UniProt to SGD ids using UniProt.wd
uniprot.ws uniprot ensembl
updated 9.3 years ago by ★ 7.2k • written 9.3 years ago by ▴ 160
3
votes
6
replies
2.8k
views
Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
annotation ensembl annotationdbi
5.8 years ago vd4mmind • 0
0
votes
6
replies
1.4k
views
ENSEMBL causing issues replicating previous results
R ENSEMBL topGO
6.3 years ago snguyen268 • 0
2
votes
6
replies
2.0k
views
biomaRt Ensembl ID query returns NA in 'ensembl_gene_id', 'ensembl_transcript_id', etc.
biomart ensembl annotation
updated 6.8 years ago by ★ 6.5k • written 6.8 years ago by ▴ 30
1
vote
5
replies
2.9k
views
Ensembl bacteria not accessible from biomaRt
biomart ensembl
updated 7.9 years ago by 25k • written 7.9 years ago by ▴ 20
8
votes
5
replies
5.2k
views
biomaRt Ensembl gene ID to multiple HGNC symbol
ensembl symbol hgnc biomart
updated 4.9 years ago by 65k • written 4.9 years ago by ▴ 100
4
votes
5
replies
1.5k
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 5.0 years ago by 65k • written 5.0 years ago by ▴ 10
0
votes
5
replies
4.6k
views
Ensembl biomaRt connection errors
software error biomart ensembl
updated 7.8 years ago by ▴ 70 • written 7.8 years ago by • 0
4
votes
5
replies
1.7k
views
ChIPpeakAnno getAnnotation request fail
chippeakanno biomart ensembl
8.3 years ago igor ▴ 40
7
votes
5
replies
6.8k
views
biomaRt server error, and mirrors do not help
ensembl biomaRt R
updated 6 months ago by • 0 • written 23 months ago by ▴ 40
0
votes
5
replies
1.7k
views
News: Ensembl 79 release is out!
Ensembl biomart release news News
updated 9.1 years ago by ★ 8.2k • written 9.1 years ago by ▴ 20
5
votes
5
replies
2.0k
views
News: Ensembl 88 is out!
ensembl ensembl mart biomart e!88 News
7.1 years ago Thomas Maurel ▴ 800
0
votes
5
replies
2.6k
views
getBM in loop
biomart ensembl curl
updated 6.3 years ago by ★ 6.5k • written 6.3 years ago by ▴ 40
0
votes
5
replies
1.5k
views
Using mgeneSim with Ensembl ids
Ensembl GOsemsim GO semantic similarity
updated 7.7 years ago by ★ 1.2k • written 7.7 years ago by ▴ 10
6
votes
5
replies
8.1k
views
biomaRt: no access to Ensembl_75 (GRCh37.p13)
biomarRt ensembl
updated 9.4 years ago by • 0 • written 9.5 years ago by • 0
2
votes
4
replies
1.6k
views
make TxDb from list of genes
R maketxdbfrombiomart maketxdbfromgranges rstudio ensembl
updated 12 months ago by • 0 • written 5.4 years ago by • 0
0
votes
4
replies
1.9k
views
biomaRT getBM error
biomart getbm ensembl
updated 6.1 years ago by ★ 6.5k • written 6.1 years ago by • 0
4
votes
4
replies
1.6k
views
biomaRt getSequence fails with genomic coordinates
biomart getSequence genomic coordinates ENSEMBL bug report
updated 4.2 years ago by ★ 6.5k • written 4.2 years ago by ▴ 10
0
votes
4
replies
1.4k
views
Error message: "Request to BioMart web service failed."
BiocManager biomaRt listMarts() ensembl Biomart
updated 4.8 years ago by ★ 6.5k • written 4.8 years ago by • 0
2
votes
4
replies
1.7k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl macaque dbsnp customprodb
updated 8.8 years ago by ▴ 50 • written 8.8 years ago by • 0
1
vote
4
replies
3.9k
views
ensembl not working...?
ensembl biomart
6.0 years ago JoeMG • 0
0
votes
4
replies
1.1k
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 4.0 years ago by 41k • written 4.0 years ago by • 0
2
votes
3
replies
11k
views
BiomaRt: protein coding transcript identification
ensembl protein coding biomart
updated 9.5 years ago by ▴ 800 • written 9.5 years ago by ▴ 120
1
vote
3
replies
2.5k
views
Convert mouse gene ids to hamster gene ids
biomart R ensembl
updated 14 months ago by ★ 3.9k • written 3.8 years ago by • 0
0
votes
3
replies
1.9k
views
How to produce a dataframe with unique ENTREZID to use in gage?
gage annotationdbi entrez ensembl
6.2 years ago colaneri ▴ 30
0
votes
3
replies
1.9k
views
DESeq2: removal of duplicated genes during statistical analysis
deseq2 gene symbol ensembl
updated 5.4 years ago by 41k • written 5.4 years ago by ▴ 10
1
vote
3
replies
2.2k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub Ensembl Mouse AnnotationHub Ensembl
4.3 years ago dmgatti ▴ 10
0
votes
3
replies
2.4k
views
biomaRt fails for M.musculus annotation, Ensembl version 80
biomart ensembl
updated 8.6 years ago by ▴ 20 • written 8.6 years ago by ▴ 80
50 results • Page 1 of 1
Recent ...
Replies
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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