Showing : BiomaRt • reset
1
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106
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News: Upcoming Ensembl API and data access changes - new blog post available
ensembl mart biomaRt ensembldb
4 days ago Ensembl_Jorge ▴ 10
0
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1
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304
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Extract snp information from genomic regions with biomaRt -> "oaries_snp"
biomaRt
updated 18 days ago by ★ 4.0k • written 3 months ago by • 0
5
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3
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408
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Issues with downloading biomaRt - SeqInfo and S4 Vectors
S4Vectors biomaRt Seqinfo
updated 29 days ago by 68k • written 29 days ago by ▴ 10
0
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1
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207
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News: Ensembl 115 has been released!
ensembl ensembldb biomaRt
written 11 weeks ago by ▴ 10
1
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3
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1.4k
views
News: Ensembl 114 / Ensembl Genomes 61 has been released!
biomaRt ensembldb
written 7 months ago by ▴ 30
1
vote
1
reply
668
views
Biomart server error
biomaRt BioMartGOGeneSets
updated 6 months ago by 68k • written 6 months ago by • 0
0
votes
3
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847
views
getBM from biomaRt inconsistencies found with .gtf files across multiple species
.gtf biomaRt Ensembl
updated 8 months ago by ★ 6.6k • written 8 months ago by ▴ 20
0
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4
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2.3k
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Ensembl site unresponsive via biomaRt
biomaRt
updated 7 months ago by • 0 • written 8 months ago by • 0
3
votes
5
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2.1k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 10 months ago by 68k • written 10 months ago by ▴ 10
0
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2
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1.6k
views
Error using useMart or useEnsembl
biomaRt
updated 10 months ago by 68k • written 10 months ago by • 0
0
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4
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1.8k
views
Biomart and ensembl not working?
ensembldb biomaRt
updated 10 months ago by 68k • written 10 months ago by • 0
3
votes
9
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2.0k
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 10 months ago by • 0 • written 11 months ago by • 0
4
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9
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2.9k
views
biomaRt rnorvegicus_gene_ensembl not available anymore
Rattus_norvegicus biomaRt
updated 11 months ago by 68k • written 13 months ago by ▴ 20
0
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0
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962
views
News: Ensembl 113 has been released
ensembl ensembldb mart biomaRt
13 months ago Ensembl_Jorge ▴ 10
0
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1
reply
821
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BiomaRt - improved access to Ensembl ?
biomaRt
updated 14 months ago by ★ 6.6k • written 14 months ago by • 0
2
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2
replies
1.7k
views
Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
biomaRt
14 months ago 2044291597 • 0
1
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3
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1.8k
views
502 error biomaRt getLDS()
ensembldb biomaRt
updated 15 months ago by 68k • written 22 months ago by ▴ 10
1
vote
4
replies
1.8k
views
BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN biomaRt
updated 13 months ago by • 0 • written 15 months ago by • 0
1
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4
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1.5k
views
How to Query Only SNPs from the biomaRt Variation Database
biomaRt
16 months ago kschecht • 0
2
votes
8
replies
3.8k
views
biomaRt getLDS error
biomaRt
16 months ago mark.dunning ▴ 20
1
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2
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1.6k
views
Issues with retrieving mouse SNP dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
biomaRt
17 months ago Svitlana ▴ 10
0
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0
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627
views
BiomaRt attribute "description" doesn't return NCBI's gene summary anymore
biomaRt
18 months ago Reese • 0
0
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2
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1.1k
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db biomaRt
18 months ago landenshanie ▴ 40
0
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0
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559
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Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets allele_freq biomaRt getBM
18 months ago Abiologist • 0
1
vote
0
replies
1.0k
views
News: Ensembl 112 has been released.
ensembldb biomaRt ensemblrelease
19 months ago Aleena_Ensembl ▴ 30
1
vote
3
replies
954
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 19 months ago by 68k • written 19 months ago by ▴ 30
2
votes
2
replies
1.6k
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
1
reply
846
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 20 months ago by 68k • written 20 months ago by • 0
0
votes
1
reply
1.9k
views
error in mapIds function
mapIds biomaRt
updated 21 months ago by 700 • written 21 months ago by • 0
0
votes
2
replies
1.5k
views
Issue with BiomaRt's getLDS: Query ERROR: caught BioMart::Exception::Query: returning undef ... missing attributes for your exportable
biomaRt
22 months ago eefernan5 • 0
3
votes
3
replies
16k
views
How to find rsID with biomaRt in R
biomaRt
updated 22 months ago by 68k • written 4.8 years ago by ▴ 10
0
votes
1
reply
701
views
biomaRt issue
biomaRt
updated 22 months ago by ★ 6.6k • written 22 months ago by • 0
1
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5
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2.2k
views
BiomaRt download data error
biomaRt
updated 22 months ago by ★ 6.6k • written 22 months ago by • 0
6
votes
9
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4.1k
views
biomaRt has encountered an unknown server error.
biomaRt host useEnsembl
updated 22 months ago by • 0 • written 22 months ago by • 0
1
vote
1
reply
2.2k
views
Error with biomaRt
biomaRt
updated 22 months ago by ★ 6.6k • written 22 months ago by • 0
4
votes
2
replies
1.3k
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 22 months ago by ★ 4.1k • written 23 months ago by • 0
2
votes
2
replies
1.6k
views
biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
biomaRt
23 months ago bd2000 ▴ 30
1
vote
0
replies
785
views
News: Ensembl 111 has been released
Ensembl biomaRt
23 months ago Benjamin ▴ 30
0
votes
2
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1.2k
views
Problem with loading ensembl version 105.
biomaRt
23 months ago RC • 0
0
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1
reply
2.2k
views
biomaRt_getBM_Failed to collect lazy table
getBM biomaRt
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
0
votes
3
replies
1.8k
views
Obtaining rsIDs with ENSG and variant ID information
rsid biomaRt
updated 2.0 years ago by ★ 3.4k • written 2.0 years ago by ▴ 30
4
votes
12
replies
2.5k
views
Ensembl down???
biomaRt
2.0 years ago bas_work ▴ 30
3
votes
2
replies
1.2k
views
biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl database
ensembl biomaRt
2.0 years ago henrydionne ▴ 10
1
vote
2
replies
2.5k
views
How to find stop codons for a list of genes
stopcodon biomaRt
2.0 years ago Marek Gierlinski ▴ 30
0
votes
10
replies
1.9k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
2.1 years ago • updated 21 months ago ScafioRuo • 0
12
votes
10
replies
16k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 20 months ago by • 0 • written 2.1 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 2.1 years ago by 53k • written 2.1 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
2.2 years ago andrew.b.kleist ▴ 10
7
votes
6
replies
9.0k
views
Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 2.2 years ago by 700 • written 3.3 years ago by ▴ 20
0
votes
2
replies
980
views
Biomart - upstream region of 'coding'
biomaRt
updated 2.2 years ago by ★ 6.6k • written 2.2 years ago by ▴ 20
1,083 results • Page 1 of 22
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
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