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BioMart
•
reset
0
votes
4
replies
87
views
biomaRt code/getBM function no longer importing 'coding' sequence via seqType argument, "Invalid attribute(s): coding" error
biomaRt
1 day ago • updated 3 hours ago
andrew.b.kleist
• 0
7
votes
4
replies
2.3k
views
Conversion of UniProt to Ensembl
biomaRt
ensembldb
UniProt.ws
updated 14 days ago by
Marcel Ramos
680 • written 13 months ago by
Recep
▴ 20
0
votes
2
replies
107
views
Biomart - upstream region of 'coding'
biomaRt
updated 18 days ago by
Mike Smith
★ 6.1k • written 19 days ago by
andrebolerbarros
▴ 20
0
votes
0
replies
104
views
Getting CDS 5'/CDS3' incomplete flags info from ENSEMBL using biomaRt
biomaRt
5 weeks ago
ali.oghabian
• 0
1
vote
5
replies
261
views
Errors with makeTxDbFromBiomart
biomaRt
updated 6 weeks ago by
James W. MacDonald
63k • written 6 weeks ago by
Jerina
▴ 10
3
votes
2
replies
310
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 6 weeks ago by
Guido Hooiveld
★ 3.7k • written 6 weeks ago by
Milan
▴ 10
0
votes
3
replies
359
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 6 weeks ago by
Hervé Pagès
16k • written 9 weeks ago by
anavmar1
• 0
1
vote
2
replies
205
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl
R
biomaRt
9 weeks ago
Miguel
• 0
0
votes
1
reply
186
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
358
views
News:
News:Ensembl 110 has been released
ensembldb
biomaRt
updated 9 weeks ago by
Michael Love
40k • written 10 weeks ago by
Benjamin
▴ 20
0
votes
1
reply
364
views
multiple filters in biomaRt
biomaRt
updated 3 months ago by
RuBBiT0
▴ 10 • written 4 months ago by
Yijing
• 0
2
votes
4
replies
411
views
Use with_go along with other filters in getBM function
Annotation
biomaRt
4 months ago • updated 3 months ago
RuBBiT0
▴ 10
1
vote
2
replies
416
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
279
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
599
views
getLDS causes "biomaRt has encountered an unexpected server error"
biomaRt
updated 4 months ago by
garryfrenchgarry
• 0 • written 5 months ago by
nhaus
• 0
0
votes
1
reply
631
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
396
views
BiomaRt: problems annotating a list of DEGs from DESeq2
biomaRt
updated 5 months ago by
Michael Love
40k • written 5 months ago by
alan.g.hudson
• 0
0
votes
2
replies
448
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt
ensembldb
RNA
ensembl
updated 5 months ago by
Johannes Rainer
★ 2.0k • written 5 months ago by
Christopher
• 0
0
votes
3
replies
377
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
371
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
532
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2
biomaRt
R
7 months ago
Dr.
• 0
0
votes
0
replies
332
views
BiomaRt - Problem to access homolog lists
biomaRt
ensembldb
7 months ago
ginie.dub
• 0
1
vote
3
replies
639
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
871
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
458
views
mmc57bl6nj_gene_ensembl biomaRt
biomaRt
8 months ago
Maryam
• 0
1
vote
3
replies
555
views
Convert Chromosome postion to gene symbol
biomaRt
ensembldb
9 months ago
mbansal
• 0
1
vote
3
replies
520
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
1.0k
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
509
views
News:
Ensembl 108 has been released!
biomaRt
ensembldb
ensembl
written 11 months ago by
Louisse
▴ 10
0
votes
3
replies
620
views
Problem installing biomaRt on mac
biomaRt
mac
updated 6 weeks ago by
15753563659
▴ 50 • written 10 months ago by
alfonsosaera
• 0
0
votes
4
replies
744
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
396
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
557
views
issue with biomaRt ENSEMBL_MART_SNP
biomaRt
updated 12 months ago by
Mike Smith
★ 6.1k • written 12 months ago by
Laurel
▴ 10
2
votes
2
replies
1.4k
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
487
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
444
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
567
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
675
views
Retrieve gene summary start/end in biomart query
biomaRt
13 months ago
rbenel
▴ 30
0
votes
0
replies
426
views
biomaRt, Ensembl, retrieve "Phenotypes" information
Ensembl
biomaRt
13 months ago
Hector
• 0
0
votes
1
reply
599
views
error in function useDataset of biomaRt
bioma
biomaRt
updated 13 months ago by
Basti
▴ 720 • written 13 months ago by
Riley Qiu
• 0
0
votes
0
replies
362
views
biomaRt, Ensembl, adding new "phenotype_source"
biomaRt
14 months ago
Hector
• 0
3
votes
2
replies
662
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
2.3k
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 14 months ago by
colantuonicarlo
• 0
0
votes
0
replies
489
views
biomaRt has encountered an unknown server error
biomaRt
14 months ago
Grace_H
• 0
0
votes
0
replies
506
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
14 months ago
04.marshal-decibel
• 0
0
votes
1
reply
642
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
583
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
15 months ago
pcantalupo
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: DiffBind handling of replicates and consensus
by
Rory Stark
★ 5.0k
You may want to try different values for the `normalize` parameter: dbObj <- dba.normalize(DBA = dbObj, library = "RiP", normalize=DBA…
Comment: DiffBind: dba.plotProfile(profiles)
by
Rory Stark
★ 5.0k
Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…
Comment: DiffBind: dba.plotProfile(profiles)
by
Dorien
▴ 10
Not really an answer as I don't know really know why , but I also had the same issue and may have found a workaround ! If I set maxSites > …
Comment: Suggested package missing from Development version of Bioconductor
by
shepherl
3.5k
Is your package in review or already in Bioconductor? Its harder if it is in review because we can't tell that the package has or can build…
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar
by
andrew.b.kleist
• 0
This worked perfectly! I was able to retrieve the sequences of interest using ```host="https://grch37.ensembl.org"``` within the useEnsembl…
Votes
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC
Comment: DiffBind: dba.plotProfile(profiles)
Normalisation of data using DESeq2 with multi-groups
Answer: Normalisation of data using DESeq2 with multi-groups
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
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