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Showing :
BioMart
•
reset
22
votes
15
replies
7.4k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 5 months ago by
Marie
▴ 10 • written 2.0 years ago by
Dina
▴ 50
4
votes
12
replies
930
views
Ensembl down???
biomaRt
4 months ago
bas_work
▴ 30
10
votes
10
replies
6.6k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 5 weeks ago by
juo5
• 0 • written 6 months ago by
Abhishek
▴ 10
0
votes
10
replies
792
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
5 months ago • updated 7 weeks ago
ScafioRuo
• 0
6
votes
9
replies
716
views
biomaRt has encountered an unknown server error.
biomaRt
host
useEnsembl
updated 12 weeks ago by
alexander3
• 0 • written 12 weeks ago by
Amparo
• 0
1
vote
7
replies
4.4k
views
Problems Installing biomaRt
biomaRt
updated 5 months ago by
James W. MacDonald
65k • written 2.0 years ago by
ksci
▴ 20
7
votes
6
replies
4.1k
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
1
vote
5
replies
590
views
Errors with makeTxDbFromBiomart
biomaRt
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
Jerina
▴ 10
7
votes
5
replies
6.9k
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
updated 6 months ago by
Ke
• 0 • written 24 months ago by
kieran.short
▴ 40
1
vote
5
replies
395
views
BiomaRt download data error
biomaRt
updated 11 weeks ago by
Mike Smith
★ 6.5k • written 11 weeks ago by
Max Bone
• 0
1
vote
4
replies
649
views
biomaRt code/getBM function no longer importing 'coding' sequence via seqType argument, "Invalid attribute(s): coding" error
biomaRt
7 months ago • updated 6 months ago
andrew.b.kleist
▴ 10
1
vote
4
replies
1.1k
views
Issue with Biomart- cannot access ensembl
biomaRT
updated 5 weeks ago by
James W. MacDonald
65k • written 4.0 years ago by
RJW63
• 0
3
votes
4
replies
1.7k
views
biomaRt error: database disk image is malformed
biomaRt
updated 11 months ago by
Emile
• 0 • written 2.5 years ago by
victorcampos1995
• 0
2
votes
4
replies
914
views
Use with_go along with other filters in getBM function
Annotation
biomaRt
11 months ago • updated 10 months ago
RuBBiT0
▴ 10
5
votes
4
replies
9.7k
views
Getting rs ids using chr coordinates | Biomart
SNP
rs id
Biomart
Chromosome
coordinates
updated 9 months ago by
James W. MacDonald
65k • written 3.7 years ago by
Mahan
• 0
0
votes
3
replies
987
views
Problem installing biomaRt on mac
biomaRt
mac
updated 8 months ago by
15753563659
▴ 50 • written 17 months ago by
alfonsosaera
• 0
0
votes
3
replies
360
views
Obtaining rsIDs with ENSG and variant ID information
rsid
biomaRt
updated 4 months ago by
Robert Castelo
★ 3.3k • written 4 months ago by
bd2000
▴ 30
0
votes
3
replies
755
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 8 months ago by
Hervé Pagès
16k • written 9 months ago by
anavmar1
• 0
0
votes
3
replies
102
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
bas_work
▴ 30
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
3
replies
459
views
determine if R package or it's dependencies functionality require internet access
biomaRt
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
Marilyn
• 0
3
votes
3
replies
9.3k
views
How to find rsID with biomaRt in R
biomaRt
updated 11 weeks ago by
James W. MacDonald
65k • written 3.1 years ago by
Federica
▴ 10
4
votes
2
replies
344
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
3
votes
2
replies
1.1k
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
2
votes
2
replies
139
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
sansan
• 0
1
vote
2
replies
590
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl
R
biomaRt
9 months ago
Miguel
• 0
0
votes
2
replies
374
views
Problem with loading ensembl version 105.
biomaRt
4 months ago
RC
• 0
1
vote
2
replies
618
views
How to find stop codons for a list of genes
stopcodon
biomaRt
5 months ago
Marek Gierlinski
▴ 30
3
votes
2
replies
410
views
biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl database
ensembl
biomaRt
5 months ago • updated 4 months ago
henrydionne
▴ 10
0
votes
2
replies
354
views
Biomart - upstream region of 'coding'
biomaRt
updated 7 months ago by
Mike Smith
★ 6.5k • written 7 months ago by
andrebolerbarros
▴ 20
1
vote
2
replies
771
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
2
replies
440
views
Issue with BiomaRt's getLDS: Query ERROR: caught BioMart::Exception::Query: returning undef ... missing attributes for your exportable
biomaRt
10 weeks ago
eefernan5
• 0
2
votes
2
replies
607
views
biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
biomaRt
3 months ago
bd2000
▴ 30
0
votes
2
replies
690
views
biomart not ound some prevous release
biomart
rnaseq
written 5.2 years ago by
jarod_v6@libero.it
▴ 40
0
votes
1
reply
1.5k
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
808
views
multiple filters in biomaRt
biomaRt
updated 10 months ago by
RuBBiT0
▴ 10 • written 11 months ago by
Yijing
• 0
1
vote
1
reply
356
views
Error with biomaRt
biomaRt
updated 3 months ago by
Mike Smith
★ 6.5k • written 3 months ago by
goldenboy
• 0
0
votes
1
reply
606
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
1
vote
1
reply
213
views
502 error biomaRt getLDS()
ensembldb
biomaRt
updated 10 weeks ago by
Robin
• 0 • written 11 weeks ago by
Pez
▴ 10
0
votes
1
reply
952
views
How to get Cytogenetic band for muscles gene by using Biomart or other tools in R
Annotation
biomaRt
ensembldb
written 2.4 years ago by
Lillian
• 0
0
votes
1
reply
670
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
1
reply
125
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
Reeya
• 0
0
votes
1
reply
207
views
biomaRt issue
biomaRt
updated 11 weeks ago by
Mike Smith
★ 6.5k • written 11 weeks ago by
Fariz
• 0
0
votes
1
reply
267
views
error in mapIds function
mapIds
biomaRt
updated 8 weeks ago by
Marcel Ramos
690 • written 8 weeks ago by
Regina
• 0
0
votes
0
replies
361
views
Getting CDS 5'/CDS3' incomplete flags info from ENSEMBL using biomaRt
biomaRt
8 months ago
ali.oghabian
• 0
1
vote
0
replies
190
views
News:
Ensembl 111 has been released
Ensembl
biomaRt
3 months ago
Benjamin
▴ 30
46 results • Page
1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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James W. MacDonald
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Gordon Smyth
50k
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to
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