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bioMart
•
reset
0
votes
0
replies
6
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
35 minutes ago
bas_work
▴ 30
1
vote
2
replies
56
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 55 minutes ago by
James W. MacDonald
65k • written 16 hours ago by
sansan
• 0
0
votes
1
reply
111
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
Reeya
• 0
0
votes
1
reply
251
views
error in mapIds function
mapIds
biomaRt
updated 7 weeks ago by
Marcel Ramos
690 • written 7 weeks ago by
Regina
• 0
0
votes
2
replies
433
views
Issue with BiomaRt's getLDS: Query ERROR: caught BioMart::Exception::Query: returning undef ... missing attributes for your exportable
biomaRt
9 weeks ago
eefernan5
• 0
3
votes
3
replies
9.2k
views
How to find rsID with biomaRt in R
biomaRt
updated 10 weeks ago by
James W. MacDonald
65k • written 3.1 years ago by
Federica
▴ 10
1
vote
1
reply
205
views
502 error biomaRt getLDS()
ensembldb
biomaRt
updated 9 weeks ago by
Robin
• 0 • written 10 weeks ago by
Pez
▴ 10
0
votes
1
reply
201
views
biomaRt issue
biomaRt
updated 10 weeks ago by
Mike Smith
★ 6.5k • written 10 weeks ago by
Fariz
• 0
1
vote
5
replies
378
views
BiomaRt download data error
biomaRt
updated 10 weeks ago by
Mike Smith
★ 6.5k • written 10 weeks ago by
Max Bone
• 0
6
votes
9
replies
688
views
biomaRt has encountered an unknown server error.
biomaRt
host
useEnsembl
updated 11 weeks ago by
alexander3
• 0 • written 11 weeks ago by
Amparo
• 0
1
vote
1
reply
337
views
Error with biomaRt
biomaRt
updated 3 months ago by
Mike Smith
★ 6.5k • written 3 months ago by
goldenboy
• 0
4
votes
2
replies
333
views
Enrichement with clusterProfiler and biomart
biomaRt
clusterProfiler
Zea_mays
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 3 months ago by
sansan
• 0
2
votes
2
replies
591
views
biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
biomaRt
3 months ago
bd2000
▴ 30
1
vote
0
replies
176
views
News:
Ensembl 111 has been released
Ensembl
biomaRt
3 months ago
Benjamin
▴ 30
0
votes
2
replies
359
views
Problem with loading ensembl version 105.
biomaRt
3 months ago
RC
• 0
0
votes
1
reply
640
views
biomaRt_getBM_Failed to collect lazy table
getBM
biomaRt
updated 4 months ago by
James W. MacDonald
65k • written 4 months ago by
ai.yaku
• 0
0
votes
3
replies
350
views
Obtaining rsIDs with ENSG and variant ID information
rsid
biomaRt
updated 4 months ago by
Robert Castelo
★ 3.2k • written 4 months ago by
bd2000
▴ 30
4
votes
12
replies
910
views
Ensembl down???
biomaRt
4 months ago
bas_work
▴ 30
3
votes
2
replies
397
views
biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl database
ensembl
biomaRt
4 months ago
henrydionne
▴ 10
1
vote
2
replies
587
views
How to find stop codons for a list of genes
stopcodon
biomaRt
4 months ago
Marek Gierlinski
▴ 30
0
votes
10
replies
786
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
5 months ago • updated 6 weeks ago
ScafioRuo
• 0
10
votes
10
replies
6.4k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 29 days ago by
juo5
• 0 • written 5 months ago by
Abhishek
▴ 10
0
votes
3
replies
451
views
determine if R package or it's dependencies functionality require internet access
biomaRt
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
Marilyn
• 0
1
vote
4
replies
639
views
biomaRt code/getBM function no longer importing 'coding' sequence via seqType argument, "Invalid attribute(s): coding" error
biomaRt
6 months ago
andrew.b.kleist
▴ 10
7
votes
6
replies
4.0k
views
Conversion of UniProt to Ensembl
biomaRt
ensembldb
UniProt.ws
updated 6 months ago by
Marcel Ramos
690 • written 20 months ago by
Recep
▴ 20
0
votes
2
replies
347
views
Biomart - upstream region of 'coding'
biomaRt
updated 7 months ago by
Mike Smith
★ 6.5k • written 7 months ago by
andrebolerbarros
▴ 20
0
votes
0
replies
351
views
Getting CDS 5'/CDS3' incomplete flags info from ENSEMBL using biomaRt
biomaRt
8 months ago
ali.oghabian
• 0
1
vote
5
replies
581
views
Errors with makeTxDbFromBiomart
biomaRt
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
Jerina
▴ 10
3
votes
2
replies
1.0k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 8 months ago by
Guido Hooiveld
★ 3.9k • written 8 months ago by
Milan
▴ 10
0
votes
3
replies
736
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 8 months ago by
Hervé Pagès
16k • written 8 months ago by
anavmar1
• 0
1
vote
2
replies
581
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl
R
biomaRt
8 months ago
Miguel
• 0
0
votes
1
reply
600
views
Trouble using biomaRt to pull pathway genes from GO
GO
biomaRt
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
cstorer
• 0
0
votes
1
reply
1.4k
views
News:
News:Ensembl 110 has been released
ensembldb
biomaRt
updated 9 months ago by
Michael Love
41k • written 9 months ago by
Benjamin
▴ 30
0
votes
1
reply
789
views
multiple filters in biomaRt
biomaRt
updated 10 months ago by
RuBBiT0
▴ 10 • written 11 months ago by
Yijing
• 0
2
votes
4
replies
903
views
Use with_go along with other filters in getBM function
Annotation
biomaRt
11 months ago • updated 10 months ago
RuBBiT0
▴ 10
1
vote
2
replies
766
views
Error: biomaRt has encountered an unexpected server error.
biomaRt
updated 10 months ago by
Mike Smith
★ 6.5k • written 11 months ago by
Yijing
• 0
0
votes
3
replies
538
views
BioMart Error message when pulling sequences
biomaRt
bioma
updated 12 months ago by
Mike Smith
★ 6.5k • written 12 months ago by
Luca
• 0
0
votes
3
replies
1.3k
views
getLDS causes "biomaRt has encountered an unexpected server error"
biomaRt
written 12 months ago by
nhaus
▴ 30
0
votes
1
reply
1.3k
views
biomaRt - NameSpace loading failed
biomaRt
bioma
updated 12 months ago by
Mike Smith
★ 6.5k • written 12 months ago by
Alessia
• 0
0
votes
3
replies
649
views
BiomaRt: problems annotating a list of DEGs from DESeq2
biomaRt
updated 12 months ago by
Michael Love
41k • written 12 months ago by
alan.g.hudson
• 0
0
votes
2
replies
1.0k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt
ensembldb
RNA
ensembl
updated 12 months ago by
Johannes Rainer
★ 2.0k • written 12 months ago by
Christopher
• 0
0
votes
3
replies
689
views
How to getting synonymous SNPs from BiomaRt before timing out?
biomaRt
SNP
updated 12 months ago by
James W. MacDonald
65k • written 13 months ago by
Damien
• 0
0
votes
2
replies
741
views
Retrieving true orthologs between species BiomaRt
Orthologs
BiomaRt
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Colin
• 0
0
votes
5
replies
2.3k
views
Is biomaRt down?
biomart
updated 13 months ago by
Xinling
• 0 • written 5.3 years ago by
ben.run974
• 0
0
votes
4
replies
927
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2
biomaRt
R
14 months ago
Dr.
• 0
0
votes
0
replies
674
views
BiomaRt - Problem to access homolog lists
biomaRt
ensembldb
14 months ago
ginie.dub
• 0
3
votes
3
replies
1.6k
views
transcript name mapping between human and mouse
biomaRt
getLDS
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Eric
▴ 20
5
votes
3
replies
1.4k
views
Problem obtaining NCBI gene IDs from Ensembl version 107
biomaRt
ensembldb
ensembl
18 months ago • updated 15 months ago
jamie.gearing
▴ 60
1
vote
4
replies
690
views
mmc57bl6nj_gene_ensembl biomaRt
biomaRt
15 months ago
Maryam
• 0
1
vote
3
replies
801
views
Convert Chromosome postion to gene symbol
biomaRt
ensembldb
16 months ago
mbansal
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 setting significant p-value
by
Dev
• 0
Sir but when I put in the data via the csv file, it was showing the gene names then but now when i set it in the form factor it is not show…
Answer: OrgDb for maize
by
James W. MacDonald
65k
``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…
Comment: Which input file is used for DGEList in EgdeR?
by
i.atanasoai
• 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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