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Showing :
Biomart
•
reset
0
votes
0
replies
841
views
Getting CDS 5'/CDS3' incomplete flags info from ENSEMBL using biomaRt
biomaRt
2.3 years ago
ali.oghabian
• 0
1
vote
5
replies
1.2k
views
Errors with makeTxDbFromBiomart
biomaRt
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
Jerina
▴ 10
3
votes
2
replies
2.8k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 2.3 years ago by
Guido Hooiveld
★ 4.1k • written 2.3 years ago by
Milan
▴ 10
0
votes
3
replies
1.7k
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 2.3 years ago by
Hervé Pagès
16k • written 2.4 years ago by
anavmar1
• 0
1
vote
2
replies
1.4k
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl
R
biomaRt
2.4 years ago
Miguel
• 0
0
votes
1
reply
1.2k
views
Trouble using biomaRt to pull pathway genes from GO
GO
biomaRt
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
cstorer
• 0
0
votes
1
reply
3.1k
views
News:
News:Ensembl 110 has been released
ensembldb
biomaRt
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
Benjamin
▴ 30
0
votes
1
reply
1.6k
views
multiple filters in biomaRt
biomaRt
updated 2.5 years ago by
RuBBiT0
▴ 10 • written 2.5 years ago by
Yijing
• 0
2
votes
4
replies
1.9k
views
Use with_go along with other filters in getBM function
Annotation
biomaRt
2.5 years ago
RuBBiT0
▴ 10
1
vote
2
replies
1.6k
views
Error: biomaRt has encountered an unexpected server error.
biomaRt
updated 2.5 years ago by
Mike Smith
★ 6.6k • written 2.5 years ago by
Yijing
• 0
0
votes
3
replies
1.1k
views
BioMart Error message when pulling sequences
biomaRt
bioma
updated 2.6 years ago by
Mike Smith
★ 6.6k • written 2.6 years ago by
Luca
• 0
0
votes
3
replies
2.8k
views
getLDS causes "biomaRt has encountered an unexpected server error"
biomaRt
written 2.6 years ago by
nhaus
▴ 70
0
votes
1
reply
2.4k
views
biomaRt - NameSpace loading failed
biomaRt
bioma
updated 2.7 years ago by
Mike Smith
★ 6.6k • written 2.7 years ago by
Alessia
• 0
0
votes
3
replies
1.3k
views
BiomaRt: problems annotating a list of DEGs from DESeq2
biomaRt
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
alan.g.hudson
• 0
0
votes
2
replies
2.5k
views
Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt
ensembldb
RNA
ensembl
updated 2.7 years ago by
Johannes Rainer
★ 2.1k • written 2.7 years ago by
Christopher
• 0
0
votes
3
replies
1.3k
views
How to getting synonymous SNPs from BiomaRt before timing out?
biomaRt
SNP
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
Damien
• 0
0
votes
2
replies
2.1k
views
Retrieving true orthologs between species BiomaRt
Orthologs
BiomaRt
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
Colin
• 0
0
votes
5
replies
3.3k
views
Is biomaRt down?
biomart
updated 2.7 years ago by
Xinling
• 0 • written 6.9 years ago by
ben.run974
• 0
0
votes
4
replies
1.7k
views
Write an annotated DESEQ2 counts CSV, pls help.
DESeq2
biomaRt
R
2.8 years ago
Dr.
• 0
0
votes
0
replies
1.2k
views
BiomaRt - Problem to access homolog lists
biomaRt
ensembldb
2.8 years ago
ginie.dub
• 0
3
votes
3
replies
3.6k
views
transcript name mapping between human and mouse
biomaRt
getLDS
updated 2.9 years ago by
James W. MacDonald
68k • written 2.9 years ago by
Eric
▴ 20
5
votes
3
replies
2.8k
views
Problem obtaining NCBI gene IDs from Ensembl version 107
biomaRt
ensembldb
ensembl
3.1 years ago • updated 2.9 years ago
jamie.gearing
▴ 60
1
vote
4
replies
1.1k
views
mmc57bl6nj_gene_ensembl biomaRt
biomaRt
2.9 years ago
Maryam
• 0
1
vote
3
replies
1.6k
views
Convert Chromosome postion to gene symbol
biomaRt
ensembldb
3.0 years ago
mbansal
• 0
1
vote
3
replies
1.2k
views
Older source of biocFileCache package
biomaRt
updated 3.0 years ago by
Mike Smith
★ 6.6k • written 3.0 years ago by
julian.konzok
• 0
1
vote
3
replies
2.0k
views
Error using biomaRt
biomaRt
updated 3.1 years ago by
Mike Smith
★ 6.6k • written 3.1 years ago by
arantes_gabriel
▴ 10
1
vote
2
replies
1.4k
views
News:
Ensembl 108 has been released!
biomaRt
ensembldb
ensembl
written 3.1 years ago by
Louisse
▴ 10
0
votes
3
replies
1.7k
views
Problem installing biomaRt on mac
biomaRt
mac
updated 2.3 years ago by
15753563659
▴ 80 • written 3.1 years ago by
alfonsosaera
• 0
0
votes
4
replies
1.8k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt
GO
ensembldb
fgsea
3.2 years ago
dario.beraldi
• 0
0
votes
1
reply
1.1k
views
Missing a list of ensembl gene dataset for some species
biomaRt
updated 3.2 years ago by
James W. MacDonald
68k • written 3.2 years ago by
ziqin
• 0
1
vote
1
reply
1.7k
views
issue with biomaRt ENSEMBL_MART_SNP
biomaRt
updated 3.2 years ago by
Mike Smith
★ 6.6k • written 3.2 years ago by
Laurel
▴ 10
2
votes
2
replies
4.2k
views
biomaRt finding transcript lenghts
biomaRt
updated 17 months ago by
niko.fleischer
• 0 • written 3.3 years ago by
Recep
▴ 20
0
votes
1
reply
1.1k
views
getBM Error with certain attribute combinations
biomaRt
ensembldb
updated 3.3 years ago by
ATpoint
★ 5.0k • written 3.3 years ago by
Luisa
• 0
2
votes
1
reply
1.1k
views
bioMart "The number of columns in the result table does not equal the number of attributes in the query."
biomaRt
updated 3.3 years ago by
Mike Smith
★ 6.6k • written 3.3 years ago by
noah.reid
▴ 10
0
votes
1
reply
1.3k
views
Problem related to `biomaRt::getBM()` during `R CMD check` execution
biomaRt
Bioconductor
updated 3.3 years ago by
James W. MacDonald
68k • written 3.3 years ago by
davide.chicco
• 0
0
votes
2
replies
1.8k
views
Retrieve gene summary start/end in biomart query
biomaRt
3.3 years ago
rbenel
▴ 50
0
votes
0
replies
984
views
biomaRt, Ensembl, retrieve "Phenotypes" information
Ensembl
biomaRt
3.3 years ago
Hector
• 0
0
votes
1
reply
1.9k
views
error in function useDataset of biomaRt
bioma
biomaRt
updated 3.3 years ago by
Basti
▴ 780 • written 3.3 years ago by
Riley Qiu
• 0
0
votes
0
replies
772
views
biomaRt, Ensembl, adding new "phenotype_source"
biomaRt
3.4 years ago
Hector
• 0
3
votes
2
replies
1.3k
views
Unable to convert Uniprot ID to Gene IDs using Biomart
biomaRt
3.4 years ago
rohitsatyam102
▴ 20
2
votes
7
replies
2.9k
views
biomaRt error during getBM
biomaRt
updated 3.4 years ago by
Mike Smith
★ 6.6k • written 3.4 years ago by
Shoma Tsubota
• 0
2
votes
1
reply
9.7k
views
using biomaRt to look up human gene symbols and map them to human ensembl ENSG IDs
biomaRt
updated 3.4 years ago by
James W. MacDonald
68k • written 3.4 years ago by
colantuonicarlo
• 0
0
votes
0
replies
1.1k
views
biomaRt has encountered an unknown server error
biomaRt
3.4 years ago
Grace_H
• 0
0
votes
0
replies
1.2k
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
3.4 years ago
04.marshal-decibel
• 0
0
votes
1
reply
1.9k
views
bioMart Sscrofa_gene_ensembl getBM() paralogues ERROR
biomaRt
ensembldb
paralogues
updated 3.4 years ago by
Malcolm Cook
★ 1.6k • written 3.4 years ago by
Zeroual
• 0
0
votes
1
reply
1.5k
views
Bioconducter can not be installed on latest RStudio
AnnotationDbi
biomaRt
Bioconductor
updated 3.4 years ago by
Mike Smith
★ 6.6k • written 3.4 years ago by
sautik87_sit
• 0
1
vote
2
replies
3.1k
views
biomaRt useMart Error in textConnection(BioMartVersion) : invalid 'text' argument
biomaRt
3.5 years ago
pcantalupo
▴ 10
0
votes
3
replies
3.6k
views
ENSEMBL to gene symbol
biomaRt
DESeq2
updated 3.5 years ago by
Guido Hooiveld
★ 4.1k • written 3.5 years ago by
Matt
• 0
2
votes
2
replies
1.7k
views
multiple annotated 3'UTR for same transcript from bioMart
biomaRt
3'UTR
3.5 years ago
adriano.biasini
▴ 10
2
votes
4
replies
20k
views
biomaRt has encountered an unexpected server error.
biomaRt
updated 3.5 years ago by
Dekel
• 0 • written 5.7 years ago by
scijrb
• 0
1,083 results • Page
2 of 22
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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