Showing : BiomaRt • reset
0
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3
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550
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getBM from biomaRt inconsistencies found with .gtf files across multiple species
.gtf biomaRt Ensembl
updated 4 weeks ago by ★ 6.6k • written 4 weeks ago by ▴ 20
0
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4
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1.1k
views
Ensembl site unresponsive via biomaRt
biomaRt
updated 3 days ago by • 0 • written 4 weeks ago by • 0
3
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5
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1.4k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 3 months ago by 68k • written 3 months ago by ▴ 10
0
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2
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1.0k
views
Error using useMart or useEnsembl
biomaRt
updated 3 months ago by 68k • written 3 months ago by • 0
0
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4
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1.2k
views
Biomart and ensembl not working?
ensembldb biomaRt
updated 3 months ago by 68k • written 3 months ago by • 0
3
votes
9
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1.1k
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 weeks ago by • 0 • written 3 months ago by • 0
4
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9
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2.3k
views
biomaRt rnorvegicus_gene_ensembl not available anymore
Rattus_norvegicus biomaRt
updated 4 months ago by 68k • written 5 months ago by ▴ 20
0
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0
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507
views
News: Ensembl 113 has been released
ensembl ensembldb mart biomaRt
6 months ago Ensembl_Jorge • 0
0
votes
1
reply
557
views
BiomaRt - improved access to Ensembl ?
biomaRt
updated 7 months ago by ★ 6.6k • written 7 months ago by • 0
2
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2
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1.5k
views
Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
biomaRt
7 months ago 2044291597 • 0
1
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3
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1.4k
views
502 error biomaRt getLDS()
ensembldb biomaRt
updated 7 months ago by 68k • written 14 months ago by ▴ 10
1
vote
4
replies
1.3k
views
BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN biomaRt
updated 5 months ago by • 0 • written 7 months ago by • 0
1
vote
4
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1.1k
views
How to Query Only SNPs from the biomaRt Variation Database
biomaRt
8 months ago kschecht • 0
2
votes
8
replies
2.7k
views
biomaRt getLDS error
biomaRt
8 months ago mark.dunning ▴ 20
1
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2
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1.2k
views
Issues with retrieving mouse SNP dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
biomaRt
10 months ago Svitlana ▴ 10
0
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0
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413
views
BiomaRt attribute "description" doesn't return NCBI's gene summary anymore
biomaRt
10 months ago Reese • 0
0
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2
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761
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db biomaRt
11 months ago landenshanie ▴ 40
0
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0
replies
393
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets allele_freq biomaRt getBM
11 months ago Abiologist • 0
1
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0
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680
views
News: Ensembl 112 has been released.
ensembldb biomaRt ensemblrelease
11 months ago Aleena ▴ 30
1
vote
3
replies
713
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 12 months ago by 68k • written 12 months ago by ▴ 30
2
votes
2
replies
1.2k
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 12 months ago by 68k • written 12 months ago by • 0
0
votes
1
reply
579
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 12 months ago by 68k • written 12 months ago by • 0
0
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1
reply
1.6k
views
error in mapIds function
mapIds biomaRt
updated 14 months ago by 700 • written 14 months ago by • 0
0
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2
replies
1.3k
views
Issue with BiomaRt's getLDS: Query ERROR: caught BioMart::Exception::Query: returning undef ... missing attributes for your exportable
biomaRt
14 months ago eefernan5 • 0
3
votes
3
replies
14k
views
How to find rsID with biomaRt in R
biomaRt
updated 14 months ago by 68k • written 4.1 years ago by ▴ 10
0
votes
1
reply
549
views
biomaRt issue
biomaRt
updated 14 months ago by ★ 6.6k • written 14 months ago by • 0
1
vote
5
replies
1.8k
views
BiomaRt download data error
biomaRt
updated 14 months ago by ★ 6.6k • written 14 months ago by • 0
6
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9
replies
3.3k
views
biomaRt has encountered an unknown server error.
biomaRt host useEnsembl
updated 15 months ago by • 0 • written 15 months ago by • 0
1
vote
1
reply
1.8k
views
Error with biomaRt
biomaRt
updated 15 months ago by ★ 6.6k • written 15 months ago by • 0
4
votes
2
replies
1.0k
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
2
votes
2
replies
1.3k
views
biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
biomaRt
15 months ago bd2000 ▴ 30
1
vote
0
replies
552
views
News: Ensembl 111 has been released
Ensembl biomaRt
15 months ago Benjamin ▴ 30
0
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2
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1.0k
views
Problem with loading ensembl version 105.
biomaRt
16 months ago RC • 0
0
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1
reply
1.8k
views
biomaRt_getBM_Failed to collect lazy table
getBM biomaRt
updated 16 months ago by 68k • written 16 months ago by • 0
0
votes
3
replies
1.4k
views
Obtaining rsIDs with ENSG and variant ID information
rsid biomaRt
updated 16 months ago by ★ 3.4k • written 17 months ago by ▴ 30
4
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12
replies
1.9k
views
Ensembl down???
biomaRt
17 months ago • updated 16 months ago bas_work ▴ 30
3
votes
2
replies
866
views
biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl database
ensembl biomaRt
17 months ago henrydionne ▴ 10
1
vote
2
replies
1.9k
views
How to find stop codons for a list of genes
stopcodon biomaRt
17 months ago Marek Gierlinski ▴ 30
0
votes
10
replies
1.5k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
17 months ago • updated 14 months ago ScafioRuo • 0
12
votes
10
replies
15k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 13 months ago by • 0 • written 18 months ago by ▴ 20
0
votes
3
replies
940
views
determine if R package or it's dependencies functionality require internet access
biomaRt
updated 18 months ago by 52k • written 18 months ago by • 0
1
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4
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1.2k
views
biomaRt code/getBM function no longer importing 'coding' sequence via seqType argument, "Invalid attribute(s): coding" error
biomaRt
19 months ago andrew.b.kleist ▴ 10
7
votes
6
replies
7.9k
views
Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 18 months ago by 700 • written 2.7 years ago by ▴ 20
0
votes
2
replies
828
views
Biomart - upstream region of 'coding'
biomaRt
updated 19 months ago by ★ 6.6k • written 19 months ago by ▴ 20
0
votes
0
replies
693
views
Getting CDS 5'/CDS3' incomplete flags info from ENSEMBL using biomaRt
biomaRt
20 months ago ali.oghabian • 0
1
vote
5
replies
999
views
Errors with makeTxDbFromBiomart
biomaRt
updated 20 months ago by 68k • written 20 months ago by ▴ 10
3
votes
2
replies
2.4k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 20 months ago by ★ 4.1k • written 20 months ago by ▴ 10
0
votes
3
replies
1.4k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 20 months ago by 16k • written 21 months ago by • 0
1
vote
2
replies
1.2k
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
21 months ago Miguel • 0
0
votes
1
reply
967
views
Trouble using biomaRt to pull pathway genes from GO
GO biomaRt
updated 21 months ago by 68k • written 21 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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