Showing : biomaRt • reset
3
votes
5
replies
1.2k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 7 weeks ago by 68k • written 7 weeks ago by ▴ 10
0
votes
2
replies
601
views
Error using useMart or useEnsembl
biomaRt
updated 7 weeks ago by 68k • written 7 weeks ago by • 0
0
votes
4
replies
684
views
Biomart and ensembl not working?
ensembldb biomaRt
updated 7 weeks ago by 68k • written 7 weeks ago by • 0
3
votes
9
replies
839
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 4 weeks ago by • 0 • written 8 weeks ago by • 0
4
votes
9
replies
2.1k
views
biomaRt rnorvegicus_gene_ensembl not available anymore
Rattus_norvegicus biomaRt
updated 12 weeks ago by 68k • written 4 months ago by ▴ 20
0
votes
0
replies
384
views
News: Ensembl 113 has been released
ensembl ensembldb mart biomaRt
4 months ago Ensembl_Jorge • 0
0
votes
1
reply
458
views
BiomaRt - improved access to Ensembl ?
biomaRt
updated 5 months ago by ★ 6.6k • written 5 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
5 months ago 2044291597 • 0
1
vote
3
replies
1.2k
views
502 error biomaRt getLDS()
ensembldb biomaRt
updated 6 months ago by 68k • written 13 months ago by ▴ 10
1
vote
4
replies
1.2k
views
BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN biomaRt
updated 4 months ago by • 0 • written 6 months ago by • 0
1
vote
4
replies
875
views
How to Query Only SNPs from the biomaRt Variation Database
biomaRt
7 months ago kschecht • 0
2
votes
8
replies
2.1k
views
biomaRt getLDS error
biomaRt
7 months ago mark.dunning ▴ 20
1
vote
2
replies
1.1k
views
Issues with retrieving mouse SNP dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
biomaRt
8 months ago Svitlana ▴ 10
0
votes
0
replies
382
views
BiomaRt attribute "description" doesn't return NCBI's gene summary anymore
biomaRt
8 months ago Reese • 0
0
votes
2
replies
649
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db biomaRt
9 months ago landenshanie ▴ 40
0
votes
0
replies
354
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets allele_freq biomaRt getBM
9 months ago Abiologist • 0
1
vote
0
replies
599
views
News: Ensembl 112 has been released.
ensembldb biomaRt ensemblrelease
10 months ago Aleena ▴ 30
1
vote
3
replies
645
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 10 months ago by 68k • written 10 months ago by ▴ 30
2
votes
2
replies
995
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
1
reply
529
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
1
reply
1.3k
views
error in mapIds function
mapIds biomaRt
updated 12 months ago by 700 • written 12 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
13k
views
How to find rsID with biomaRt in R
biomaRt
updated 13 months ago by 68k • written 4.0 years ago by ▴ 10
0
votes
1
reply
524
views
biomaRt issue
biomaRt
updated 13 months ago by ★ 6.6k • written 13 months ago by • 0
1
vote
5
replies
1.6k
views
BiomaRt download data error
biomaRt
updated 13 months ago by ★ 6.6k • written 13 months ago by • 0
6
votes
9
replies
2.9k
views
biomaRt has encountered an unknown server error.
biomaRt host useEnsembl
updated 13 months ago by • 0 • written 13 months ago by • 0
1
vote
1
reply
1.6k
views
Error with biomaRt
biomaRt
updated 13 months ago by ★ 6.6k • written 13 months ago by • 0
4
votes
2
replies
952
views
Enrichement with clusterProfiler and biomart
biomaRt clusterProfiler Zea_mays
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
2
votes
2
replies
1.2k
views
biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
biomaRt
14 months ago • updated 13 months ago bd2000 ▴ 30
1
vote
0
replies
513
views
News: Ensembl 111 has been released
Ensembl biomaRt
14 months ago Benjamin ▴ 30
0
votes
2
replies
974
views
Problem with loading ensembl version 105.
biomaRt
14 months ago RC • 0
0
votes
1
reply
1.6k
views
biomaRt_getBM_Failed to collect lazy table
getBM biomaRt
updated 15 months ago by 68k • written 15 months ago by • 0
0
votes
3
replies
1.3k
views
Obtaining rsIDs with ENSG and variant ID information
rsid biomaRt
updated 15 months ago by ★ 3.4k • written 15 months ago by ▴ 30
4
votes
12
replies
1.8k
views
Ensembl down???
biomaRt
15 months ago bas_work ▴ 30
3
votes
2
replies
807
views
biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl database
ensembl biomaRt
15 months ago henrydionne ▴ 10
1
vote
2
replies
1.7k
views
How to find stop codons for a list of genes
stopcodon biomaRt
15 months ago Marek Gierlinski ▴ 30
0
votes
10
replies
1.4k
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
16 months ago • updated 12 months ago ScafioRuo • 0
12
votes
10
replies
14k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 11 months ago by • 0 • written 16 months ago by ▴ 20
0
votes
3
replies
880
views
determine if R package or it's dependencies functionality require internet access
biomaRt
updated 16 months ago by 52k • written 16 months ago by • 0
1
vote
4
replies
1.1k
views
biomaRt code/getBM function no longer importing 'coding' sequence via seqType argument, "Invalid attribute(s): coding" error
biomaRt
17 months ago andrew.b.kleist ▴ 10
7
votes
6
replies
7.2k
views
Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 17 months ago by 700 • written 2.6 years ago by ▴ 20
0
votes
2
replies
778
views
Biomart - upstream region of 'coding'
biomaRt
updated 18 months ago by ★ 6.6k • written 18 months ago by ▴ 20
0
votes
0
replies
663
views
Getting CDS 5'/CDS3' incomplete flags info from ENSEMBL using biomaRt
biomaRt
18 months ago ali.oghabian • 0
1
vote
5
replies
954
views
Errors with makeTxDbFromBiomart
biomaRt
updated 19 months ago by 68k • written 19 months ago by ▴ 10
3
votes
2
replies
2.2k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 19 months ago by ★ 4.1k • written 19 months ago by ▴ 10
0
votes
3
replies
1.4k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 19 months ago by 16k • written 19 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
19 months ago Miguel • 0
0
votes
1
reply
922
views
Trouble using biomaRt to pull pathway genes from GO
GO biomaRt
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
1
reply
2.7k
views
News: News:Ensembl 110 has been released
ensembldb biomaRt
updated 19 months ago by 43k • written 20 months ago by ▴ 30
0
votes
1
reply
1.3k
views
multiple filters in biomaRt
biomaRt
updated 21 months ago by ▴ 10 • written 21 months ago by • 0
50 results • Page 1 of 1
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Replies
Comment: sesameDataCache is not work properly on my system by Samreen • 0
Any luck with this? I have tried all of the above and it still doesn't work. This is my session info and I'm on a cluster computing environ…
Answer: Using tximport for kallisto aligned TOIL data by James W. MacDonald 68k
If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
Answer: Reading gene expression data in GPR format and converting it to xlsx format by James W. MacDonald 68k
Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Comment: concentration tables suitable as input for new packages? by wilkinson • 0
I am grateful for your response. Software such as "Spectra" may parse MS-data to generate tables of concentrations, for instance. But inste…
Comment: Removing UTR from GTF for gene quantification by ATpoint ★ 4.7k
Consider asking at biostars or bioinformatics reddit, since this is not directly related to a Bioconductor problem. Anyway, a couple of th…
Votes
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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