Showing : BiomaRt • reset
0
votes
3
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497
views
getBM from biomaRt inconsistencies found with .gtf files across multiple species
.gtf biomaRt Ensembl
updated 11 days ago by ★ 6.6k • written 12 days ago by ▴ 20
0
votes
5
replies
793
views
Ensembl site unresponsive via biomaRt
biomaRt
updated 2 days ago by • 0 • written 13 days ago by • 0
3
votes
5
replies
1.3k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 11 weeks ago by 68k • written 11 weeks ago by ▴ 10
0
votes
2
replies
875
views
Error using useMart or useEnsembl
biomaRt
updated 11 weeks ago by 68k • written 11 weeks ago by • 0
0
votes
4
replies
1.0k
views
Biomart and ensembl not working?
ensembldb biomaRt
updated 11 weeks ago by 68k • written 11 weeks ago by • 0
3
votes
9
replies
1.0k
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 8 weeks ago by • 0 • written 12 weeks ago by • 0
4
votes
9
replies
2.2k
views
biomaRt rnorvegicus_gene_ensembl not available anymore
Rattus_norvegicus biomaRt
updated 3 months ago by 68k • written 5 months ago by ▴ 20
0
votes
0
replies
444
views
News: Ensembl 113 has been released
ensembl ensembldb mart biomaRt
5 months ago Ensembl_Jorge • 0
0
votes
1
reply
525
views
BiomaRt - improved access to Ensembl ?
biomaRt
updated 6 months ago by ★ 6.6k • written 6 months ago by • 0
2
votes
2
replies
1.4k
views
Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
biomaRt
6 months ago 2044291597 • 0
1
vote
3
replies
1.3k
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
replies
1.0k
views
How to Query Only SNPs from the biomaRt Variation Database
biomaRt
8 months ago kschecht • 0
2
votes
8
replies
2.5k
views
biomaRt getLDS error
biomaRt
8 months ago mark.dunning ▴ 20
1
vote
2
replies
1.2k
views
Issues with retrieving mouse SNP dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
biomaRt
9 months ago Svitlana ▴ 10
0
votes
0
replies
397
views
BiomaRt attribute "description" doesn't return NCBI's gene summary anymore
biomaRt
9 months ago Reese • 0
0
votes
2
replies
722
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db biomaRt
10 months ago landenshanie ▴ 40
0
votes
0
replies
370
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets allele_freq biomaRt getBM
10 months ago Abiologist • 0
1
vote
0
replies
641
views
News: Ensembl 112 has been released.
ensembldb biomaRt ensemblrelease
10 months ago Aleena ▴ 30
1
vote
3
replies
687
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 11 months ago by 68k • written 11 months ago by ▴ 30
2
votes
2
replies
1.1k
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
1
reply
555
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 12 months ago by 68k • written 12 months ago by • 0
0
votes
1
reply
1.5k
views
error in mapIds function
mapIds biomaRt
updated 13 months ago by 700 • written 13 months ago by • 0
0
votes
2
replies
1.2k
views
Issue with BiomaRt's getLDS: Query ERROR: caught BioMart::Exception::Query: returning undef ... missing attributes for your exportable
biomaRt
13 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
537
views
biomaRt issue
biomaRt
updated 14 months ago by ★ 6.6k • written 14 months ago by • 0
1
vote
5
replies
1.7k
views
BiomaRt download data error
biomaRt
updated 14 months ago by ★ 6.6k • written 14 months ago by • 0
6
votes
9
replies
3.1k
views
biomaRt has encountered an unknown server error.
biomaRt host useEnsembl
updated 14 months ago by • 0 • written 14 months ago by • 0
1
vote
1
reply
1.7k
views
Error with biomaRt
biomaRt
updated 14 months ago by ★ 6.6k • written 14 months ago by • 0
4
votes
2
replies
989
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
2
votes
2
replies
1.3k
views
biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
biomaRt
14 months ago bd2000 ▴ 30
1
vote
0
replies
532
views
News: Ensembl 111 has been released
Ensembl biomaRt
15 months ago Benjamin ▴ 30
0
votes
2
replies
1.0k
views
Problem with loading ensembl version 105.
biomaRt
15 months ago RC • 0
0
votes
1
reply
1.7k
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 16 months ago by ▴ 30
4
votes
12
replies
1.9k
views
Ensembl down???
biomaRt
16 months ago bas_work ▴ 30
3
votes
2
replies
843
views
biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl database
ensembl biomaRt
16 months ago henrydionne ▴ 10
1
vote
2
replies
1.8k
views
How to find stop codons for a list of genes
stopcodon biomaRt
16 months ago Marek Gierlinski ▴ 30
0
votes
10
replies
1.5k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
16 months ago • updated 13 months ago ScafioRuo • 0
12
votes
10
replies
14k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 12 months ago by • 0 • written 17 months ago by ▴ 20
0
votes
3
replies
911
views
determine if R package or it's dependencies functionality require internet access
biomaRt
updated 17 months ago by 52k • written 17 months ago by • 0
1
vote
4
replies
1.2k
views
biomaRt code/getBM function no longer importing 'coding' sequence via seqType argument, "Invalid attribute(s): coding" error
biomaRt
18 months ago andrew.b.kleist ▴ 10
7
votes
6
replies
7.6k
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
810
views
Biomart - upstream region of 'coding'
biomaRt
updated 19 months ago by ★ 6.6k • written 19 months ago by ▴ 20
0
votes
0
replies
684
views
Getting CDS 5'/CDS3' incomplete flags info from ENSEMBL using biomaRt
biomaRt
19 months ago ali.oghabian • 0
1
vote
5
replies
981
views
Errors with makeTxDbFromBiomart
biomaRt
updated 20 months ago by 68k • written 20 months ago by ▴ 10
3
votes
2
replies
2.3k
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 20 months ago by • 0
1
vote
2
replies
1.1k
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
20 months ago Miguel • 0
0
votes
1
reply
944
views
Trouble using biomaRt to pull pathway genes from GO
GO biomaRt
updated 20 months ago by 68k • written 20 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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