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Showing :
biomart
•
reset
1
vote
4
replies
237
views
biomaRt code/getBM function no longer importing 'coding' sequence via seqType argument, "Invalid attribute(s): coding" error
biomaRt
6 days ago • updated 5 days ago
andrew.b.kleist
▴ 10
7
votes
4
replies
2.4k
views
Conversion of UniProt to Ensembl
biomaRt
ensembldb
UniProt.ws
updated 19 days ago by
Marcel Ramos
680 • written 13 months ago by
Recep
▴ 20
0
votes
2
replies
114
views
Biomart - upstream region of 'coding'
biomaRt
updated 23 days ago by
Mike Smith
★ 6.1k • written 24 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
108
views
Getting CDS 5'/CDS3' incomplete flags info from ENSEMBL using biomaRt
biomaRt
6 weeks ago
ali.oghabian
• 0
1
vote
5
replies
267
views
Errors with makeTxDbFromBiomart
biomaRt
updated 7 weeks ago by
James W. MacDonald
63k • written 7 weeks ago by
Jerina
▴ 10
3
votes
2
replies
320
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 7 weeks ago by
Guido Hooiveld
★ 3.7k • written 7 weeks ago by
Milan
▴ 10
0
votes
3
replies
364
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 7 weeks ago by
Hervé Pagès
16k • written 10 weeks ago by
anavmar1
• 0
1
vote
2
replies
212
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl
R
biomaRt
10 weeks ago • updated 9 weeks ago
Miguel
• 0
0
votes
1
reply
189
views
Trouble using biomaRt to pull pathway genes from GO
GO
biomaRt
updated 10 weeks ago by
James W. MacDonald
63k • written 10 weeks ago by
cstorer
• 0
0
votes
1
reply
374
views
News:
News:Ensembl 110 has been released
ensembldb
biomaRt
updated 10 weeks ago by
Michael Love
40k • written 11 weeks ago by
Benjamin
▴ 20
0
votes
1
reply
369
views
multiple filters in biomaRt
biomaRt
updated 3 months ago by
RuBBiT0
▴ 10 • written 4 months ago by
Yijing
• 0
2
votes
4
replies
419
views
Use with_go along with other filters in getBM function
Annotation
biomaRt
4 months ago
RuBBiT0
▴ 10
1
vote
2
replies
418
views
Error: biomaRt has encountered an unexpected server error.
biomaRt
updated 4 months ago by
Mike Smith
★ 6.1k • written 4 months ago by
Yijing
• 0
0
votes
3
replies
285
views
BioMart Error message when pulling sequences
biomaRt
bioma
updated 5 months ago by
Mike Smith
★ 6.1k • written 5 months ago by
Luca
• 0
0
votes
2
replies
606
views
getLDS causes "biomaRt has encountered an unexpected server error"
biomaRt
updated 5 months ago by
garryfrenchgarry
• 0 • written 5 months ago by
nhaus
• 0
0
votes
1
reply
645
views
biomaRt - NameSpace loading failed
biomaRt
bioma
updated 5 months ago by
Mike Smith
★ 6.1k • written 5 months ago by
Alessia
• 0
0
votes
3
replies
400
views
BiomaRt: problems annotating a list of DEGs from DESeq2
biomaRt
updated 5 months ago by
Michael Love
40k • written 6 months ago by
alan.g.hudson
• 0
0
votes
2
replies
456
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt
ensembldb
RNA
ensembl
updated 6 months ago by
Johannes Rainer
★ 2.0k • written 6 months ago by
Christopher
• 0
0
votes
3
replies
382
views
How to getting synonymous SNPs from BiomaRt before timing out?
biomaRt
SNP
updated 6 months ago by
James W. MacDonald
63k • written 6 months ago by
Damien
• 0
0
votes
2
replies
376
views
Retrieving true orthologs between species BiomaRt
Orthologs
BiomaRt
updated 6 months ago by
James W. MacDonald
63k • written 6 months ago by
Colin
• 0
0
votes
5
replies
1.9k
views
Is biomaRt down?
biomart
updated 6 months ago by
Xinling
• 0 • written 4.7 years ago by
ben.run974
• 0
0
votes
4
replies
538
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2
biomaRt
R
7 months ago
Dr.
• 0
0
votes
0
replies
335
views
BiomaRt - Problem to access homolog lists
biomaRt
ensembldb
7 months ago
ginie.dub
• 0
1
vote
3
replies
646
views
transcript name mapping between human and mouse
biomaRt
getLDS
updated 8 months ago by
James W. MacDonald
63k • written 8 months ago by
Eric
• 0
5
votes
3
replies
878
views
Problem obtaining NCBI gene IDs from Ensembl version 107
biomaRt
ensembldb
ensembl
11 months ago • updated 8 months ago
jamie.gearing
▴ 60
1
vote
4
replies
461
views
mmc57bl6nj_gene_ensembl biomaRt
biomaRt
9 months ago • updated 8 months ago
Maryam
• 0
1
vote
3
replies
559
views
Convert Chromosome postion to gene symbol
biomaRt
ensembldb
9 months ago
mbansal
• 0
1
vote
3
replies
526
views
Older source of biocFileCache package
biomaRt
updated 10 months ago by
Mike Smith
★ 6.1k • written 10 months ago by
julian.konzok
• 0
1
vote
3
replies
1.1k
views
Error using biomaRt
biomaRt
updated 10 months ago by
Mike Smith
★ 6.1k • written 10 months ago by
arantes_gabriel
▴ 10
1
vote
2
replies
515
views
News:
Ensembl 108 has been released!
biomaRt
ensembldb
ensembl
written 11 months ago by
Louisse
▴ 10
0
votes
3
replies
634
views
Problem installing biomaRt on mac
biomaRt
mac
updated 7 weeks ago by
15753563659
▴ 50 • written 10 months ago by
alfonsosaera
• 0
0
votes
4
replies
747
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt
GO
ensembldb
fgsea
12 months ago
dario.beraldi
• 0
0
votes
1
reply
400
views
Missing a list of ensembl gene dataset for some species
biomaRt
updated 12 months ago by
James W. MacDonald
63k • written 12 months ago by
ziqin
• 0
1
vote
1
reply
563
views
issue with biomaRt ENSEMBL_MART_SNP
biomaRt
updated 13 months ago by
Mike Smith
★ 6.1k • written 13 months ago by
Laurel
▴ 10
2
votes
2
replies
1.5k
views
biomaRt finding transcript lenghts
biomaRt
updated 13 months ago by
Kevin Blighe
3.8k • written 13 months ago by
Recep
▴ 20
0
votes
1
reply
490
views
getBM Error with certain attribute combinations
biomaRt
ensembldb
updated 13 months ago by
ATpoint
★ 3.4k • written 13 months ago by
Luisa
• 0
2
votes
1
reply
449
views
bioMart "The number of columns in the result table does not equal the number of attributes in the query."
biomaRt
updated 13 months ago by
Mike Smith
★ 6.1k • written 13 months ago by
noah.reid
▴ 10
0
votes
1
reply
571
views
Problem related to `biomaRt::getBM()` during `R CMD check` execution
biomaRt
Bioconductor
updated 13 months ago by
James W. MacDonald
63k • written 13 months ago by
davide.chicco
• 0
0
votes
2
replies
676
views
Retrieve gene summary start/end in biomart query
biomaRt
13 months ago
rbenel
▴ 30
0
votes
0
replies
432
views
biomaRt, Ensembl, retrieve "Phenotypes" information
Ensembl
biomaRt
13 months ago
Hector
• 0
0
votes
1
reply
610
views
error in function useDataset of biomaRt
bioma
biomaRt
updated 14 months ago by
Basti
▴ 720 • written 14 months ago by
Riley Qiu
• 0
0
votes
0
replies
367
views
biomaRt, Ensembl, adding new "phenotype_source"
biomaRt
14 months ago
Hector
• 0
3
votes
2
replies
665
views
Unable to convert Uniprot ID to Gene IDs using Biomart
biomaRt
14 months ago
rohitsatyam102
▴ 20
2
votes
7
replies
1.3k
views
biomaRt error during getBM
biomaRt
updated 14 months ago by
Mike Smith
★ 6.1k • written 14 months ago by
Shoma Tsubota
• 0
1
vote
1
reply
2.4k
views
using biomaRt to look up human gene symbols and map them to human ensembl ENSG IDs
biomaRt
updated 14 months ago by
James W. MacDonald
63k • written 15 months ago by
colantuonicarlo
• 0
0
votes
0
replies
495
views
biomaRt has encountered an unknown server error
biomaRt
15 months ago
Grace_H
• 0
0
votes
0
replies
509
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
15 months ago
04.marshal-decibel
• 0
0
votes
1
reply
652
views
bioMart Sscrofa_gene_ensembl getBM() paralogues ERROR
biomaRt
ensembldb
paralogues
updated 15 months ago by
Malcolm Cook
★ 1.6k • written 15 months ago by
Zeroual
• 0
0
votes
1
reply
590
views
Bioconducter can not be installed on latest RStudio
AnnotationDbi
biomaRt
Bioconductor
updated 15 months ago by
Mike Smith
★ 6.1k • written 15 months ago by
sautik87_sit
• 0
1
vote
2
replies
1.3k
views
biomaRt useMart Error in textConnection(BioMartVersion) : invalid 'text' argument
biomaRt
16 months ago
pcantalupo
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: tximport error: vroom
by
Michael Love
40k
Check that they all have same number of lines. I guess one of them was interrupted while writing out and may need to be re-run (Salmon).
Comment: tximport error: vroom
by
Kevin Blighe
3.8k
Cross-posted: https://www.biostars.org/p/9576578/
Comment: Exporting DESeq2 filtered results
by
James W. MacDonald
63k
I am interested to know what part of my response you found rude. I asked nicely that you don't add to ancient posts, said your post isn't r…
Comment: Speeding up of DelayedArray::write_block()
by
Hervé Pagès
16k
> I can imagine writing a sparse high-dimensional array in HDF5, but I'm still not sure how to implement the part where it is read and imme…
Comment: Speeding up of DelayedArray::write_block()
by
Hervé Pagès
16k
Not in BioC 3.18. At some point (e.g. in 6 months) they will be deprecated, then 6 months later (i.e. in 1 year) they will be defunct, then…
Votes
Unclear of calculating correlations with case+control samples together
Answer: Error MakeOrgPackagefromNCBI
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
A: BiomaRt Arabidopsis genome unavailable
Answer: enrichKEGG
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