Showing : BioMart • reset
2
votes
4
replies
206
views
Converting Probe IDs to HGNC symbols
Annotation biomaRt GEOquery
written 13 days ago by ▴ 10
0
votes
5
replies
2.8k
views
Ensembl site unresponsive via biomaRt
biomaRt
written 9 months ago by • 0
1
vote
1
reply
262
views
News: Upcoming Ensembl API and data access changes - new blog post available
ensembl mart biomaRt ensembldb
written 6 weeks ago by ▴ 10
0
votes
1
reply
380
views
Extract snp information from genomic regions with biomaRt -> "oaries_snp"
biomaRt
updated 8 weeks ago by ★ 4.0k • written 4 months ago by • 0
5
votes
3
replies
533
views
Issues with downloading biomaRt - SeqInfo and S4 Vectors
S4Vectors biomaRt Seqinfo
updated 10 weeks ago by 68k • written 10 weeks ago by ▴ 10
0
votes
1
reply
270
views
News: Ensembl 115 has been released!
ensembl ensembldb biomaRt
written 4 months ago by ▴ 10
1
vote
3
replies
1.5k
views
News: Ensembl 114 / Ensembl Genomes 61 has been released!
biomaRt ensembldb
written 8 months ago by ▴ 30
1
vote
1
reply
705
views
Biomart server error
biomaRt BioMartGOGeneSets
updated 7 months ago by 68k • written 7 months ago by • 0
0
votes
3
replies
895
views
getBM from biomaRt inconsistencies found with .gtf files across multiple species
.gtf biomaRt Ensembl
updated 9 months ago by ★ 6.6k • written 9 months ago by ▴ 20
3
votes
5
replies
2.3k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 12 months ago by 68k • written 12 months ago by ▴ 10
0
votes
2
replies
1.9k
views
Error using useMart or useEnsembl
biomaRt
updated 12 months ago by 68k • written 12 months ago by • 0
0
votes
4
replies
2.2k
views
Biomart and ensembl not working?
ensembldb biomaRt
updated 12 months ago by 68k • written 12 months ago by • 0
3
votes
9
replies
2.3k
views
Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) returning drastically different numbers of transcripts
AnnotationDbi EnsDb.Mmusculus.v79 biomaRt org.Mm.eg.db
updated 11 months ago by • 0 • written 12 months ago by • 0
4
votes
9
replies
3.1k
views
biomaRt rnorvegicus_gene_ensembl not available anymore
Rattus_norvegicus biomaRt
updated 13 months ago by 68k • written 14 months ago by ▴ 20
0
votes
0
replies
1.1k
views
News: Ensembl 113 has been released
ensembl ensembldb mart biomaRt
15 months ago Ensembl_Jorge ▴ 10
0
votes
1
reply
900
views
BiomaRt - improved access to Ensembl ?
biomaRt
updated 15 months ago by ★ 6.6k • written 15 months ago by • 0
2
votes
2
replies
1.8k
views
Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
biomaRt
15 months ago 2044291597 • 0
1
vote
3
replies
2.0k
views
502 error biomaRt getLDS()
ensembldb biomaRt
updated 16 months ago by 68k • written 23 months ago by ▴ 10
1
vote
4
replies
2.0k
views
BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN biomaRt
updated 14 months ago by • 0 • written 16 months ago by • 0
1
vote
4
replies
1.6k
views
How to Query Only SNPs from the biomaRt Variation Database
biomaRt
17 months ago kschecht • 0
2
votes
8
replies
4.0k
views
biomaRt getLDS error
biomaRt
17 months ago mark.dunning ▴ 20
1
vote
2
replies
1.6k
views
Issues with retrieving mouse SNP dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
biomaRt
19 months ago • updated 18 months ago Svitlana ▴ 10
0
votes
0
replies
666
views
BiomaRt attribute "description" doesn't return NCBI's gene summary anymore
biomaRt
19 months ago Reese • 0
0
votes
2
replies
1.1k
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db biomaRt
20 months ago landenshanie ▴ 40
0
votes
0
replies
605
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets allele_freq biomaRt getBM
20 months ago Abiologist • 0
1
vote
0
replies
1.1k
views
News: Ensembl 112 has been released.
ensembldb biomaRt ensemblrelease
20 months ago Aleena_Ensembl ▴ 30
1
vote
3
replies
988
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 21 months ago by 68k • written 21 months ago by ▴ 30
2
votes
2
replies
1.8k
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
1
reply
921
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
1
reply
2.0k
views
error in mapIds function
mapIds biomaRt
updated 23 months ago by 700 • written 23 months ago by • 0
0
votes
2
replies
1.6k
views
Issue with BiomaRt's getLDS: Query ERROR: caught BioMart::Exception::Query: returning undef ... missing attributes for your exportable
biomaRt
23 months ago eefernan5 • 0
3
votes
3
replies
17k
views
How to find rsID with biomaRt in R
biomaRt
updated 23 months ago by 68k • written 4.9 years ago by ▴ 10
0
votes
1
reply
753
views
biomaRt issue
biomaRt
updated 23 months ago by ★ 6.6k • written 23 months ago by • 0
1
vote
5
replies
2.3k
views
BiomaRt download data error
biomaRt
updated 23 months ago by ★ 6.6k • written 23 months ago by • 0
6
votes
9
replies
4.3k
views
biomaRt has encountered an unknown server error.
biomaRt host useEnsembl
updated 23 months ago by • 0 • written 23 months ago by • 0
1
vote
1
reply
2.3k
views
Error with biomaRt
biomaRt
updated 2.0 years ago by ★ 6.6k • written 2.0 years ago by • 0
4
votes
2
replies
1.4k
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 2.0 years ago by ★ 4.1k • written 2.0 years ago by • 0
2
votes
2
replies
1.6k
views
biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
biomaRt
2.0 years ago bd2000 ▴ 30
1
vote
0
replies
829
views
News: Ensembl 111 has been released
Ensembl biomaRt
2.0 years ago Benjamin ▴ 30
0
votes
2
replies
1.3k
views
Problem with loading ensembl version 105.
biomaRt
2.1 years ago RC • 0
0
votes
1
reply
2.2k
views
biomaRt_getBM_Failed to collect lazy table
getBM biomaRt
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
3
replies
2.0k
views
Obtaining rsIDs with ENSG and variant ID information
rsid biomaRt
updated 2.1 years ago by ★ 3.4k • written 2.1 years ago by ▴ 30
4
votes
12
replies
2.6k
views
Ensembl down???
biomaRt
2.1 years ago bas_work ▴ 30
3
votes
2
replies
1.3k
views
biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl database
ensembl biomaRt
2.2 years ago • updated 2.1 years ago henrydionne ▴ 10
1
vote
2
replies
2.7k
views
How to find stop codons for a list of genes
stopcodon biomaRt
2.2 years ago Marek Gierlinski ▴ 30
0
votes
10
replies
2.0k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
2.2 years ago • updated 22 months ago ScafioRuo • 0
12
votes
10
replies
16k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 22 months ago by • 0 • written 2.2 years ago by ▴ 20
0
votes
3
replies
1.2k
views
determine if R package or it's dependencies functionality require internet access
biomaRt
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
1
vote
4
replies
1.5k
views
biomaRt code/getBM function no longer importing 'coding' sequence via seqType argument, "Invalid attribute(s): coding" error
biomaRt
2.3 years ago andrew.b.kleist ▴ 10
7
votes
6
replies
9.4k
views
Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 2.3 years ago by 700 • written 3.4 years ago by ▴ 20
1,084 results • Page 1 of 22
Recent ...
Replies
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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