Showing : Biomart • reset
0
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2
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5.2k
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Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
biomaRt AnnotationForge
3.5 years ago Lan Anh • 0
0
votes
1
reply
7.1k
views
biomaRt getLDS server error
biomaRt Bioma
3.6 years ago floriandeckert ▴ 30
4
votes
5
replies
4.2k
views
biomart getLDS giving errors.
biomaRt
3.6 years ago hnthirim ▴ 10
8
votes
5
replies
11k
views
biomaRt server error, and mirrors do not help
ensembl biomaRt R
updated 12 months ago by • 0 • written 3.6 years ago by ▴ 50
2
votes
2
replies
4.5k
views
Problems with biomaRt's getLDS
biomaRt
updated 3.5 years ago by • 0 • written 3.7 years ago by ▴ 10
22
votes
15
replies
12k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 2.1 years ago by ▴ 10 • written 3.7 years ago by ▴ 50
2
votes
8
replies
4.1k
views
biomaRt : No lock file for BiocFileCache
BiocFileCache biomaRt
updated 3.6 years ago by 25k • written 3.6 years ago by ▴ 60
2
votes
0
replies
1.1k
views
News: News:Ensembl 106 has just been released!
ensembl biomaRt ensembldb
3.7 years ago Benjamin ▴ 30
1
vote
7
replies
7.4k
views
Problems Installing biomaRt
biomaRt
updated 2.1 years ago by 68k • written 3.7 years ago by ▴ 20
2
votes
5
replies
2.5k
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
3.8 years ago Marianna ▴ 20
2
votes
3
replies
1.4k
views
Again, query error when trying to retrieve attributes from Phytozome via BiomaRt
Zea_mays Attributes biomaRt Phytozome
updated 3.8 years ago by • 0 • written 3.9 years ago by ▴ 10
0
votes
3
replies
2.7k
views
biomaRT getBM() get stuck
biomaRt getbm ensembl
updated 3.9 years ago by ★ 6.6k • written 3.9 years ago by • 0
0
votes
1
reply
1.4k
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 3.9 years ago by ★ 5.0k • written 3.9 years ago by • 0
0
votes
2
replies
2.3k
views
Can't convert dog ensembl IDs into gene names
biomaRt ensembldb
updated 4.0 years ago by ★ 5.0k • written 4.0 years ago by • 0
1
vote
0
replies
1.2k
views
News: Ensembl 105 has just been released!
ensembl biomaRt ensembldb
4.0 years ago mchakiachvili ▴ 20
0
votes
1
reply
1.7k
views
Calculating dn/ds ratios
biomaRt
updated 4.0 years ago by ★ 6.6k • written 4.0 years ago by • 0
0
votes
2
replies
1.1k
views
Why does biomart have multiple positions for the same gene
biomaRt
4.0 years ago adeler001 • 0
0
votes
1
reply
829
views
biomaRt query interrupted "expected a character string of length 1."
biomaRt
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
0
votes
1
reply
1.5k
views
How to get Cytogenetic band for muscles gene by using Biomart or other tools in R
Annotation biomaRt ensembldb
written 4.0 years ago by • 0
1
vote
2
replies
1.6k
views
biomaRt connection error
biomaRt
updated 4.1 years ago by ★ 6.6k • written 4.1 years ago by ★ 5.0k
0
votes
8
replies
2.3k
views
Annotating DESeq2 Differential Expression Results
biomaRt DESeq2
4.1 years ago adeler001 • 0
0
votes
0
replies
1.4k
views
Error with getBM: 'The query to the BioMart webservice returned an invalid result.'
process annotationTools AnnotationFilter Annotation biomaRt
4.1 years ago Shane • 0
0
votes
3
replies
1.7k
views
ENSEMBL BIOMART INTERFACE DOWN?
biomaRt
updated 4.1 years ago by ★ 6.6k • written 4.1 years ago by • 0
2
votes
1
reply
3.7k
views
Specify hg19 in using biomaRt getBM function
biomaRt biom
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
1
vote
3
replies
1.5k
views
useEnsemblGenomes not found
biomaRt
4.1 years ago lessismore ▴ 20
2
votes
3
replies
2.5k
views
biomart query in R is not matching ensembl website - missing results
ensembldb biomaRt
updated 4.2 years ago by ★ 6.6k • written 4.2 years ago by • 0
4
votes
4
replies
2.6k
views
biomaRt error: database disk image is malformed
biomaRt
updated 2.5 years ago by • 0 • written 4.2 years ago by ▴ 10
0
votes
1
reply
4.9k
views
Error in curl; timeout when using biomaRt
biomaRt bioma
updated 4.2 years ago by ★ 6.6k • written 4.2 years ago by ▴ 10
0
votes
1
reply
2.5k
views
Retrieve isoform sequences for a protein from UniProt
UniProt.ws biomaRt
updated 4.3 years ago by ★ 6.6k • written 4.3 years ago by ▴ 10
0
votes
2
replies
1.7k
views
Ensembl archive challenges
biomaRt
updated 4.3 years ago by ★ 6.6k • written 4.3 years ago by • 0
1
vote
1
reply
2.7k
views
Error in curl; timeout when using biomaRt
biomaRt curl timeout getBM Bioconductor
updated 4.3 years ago by ★ 1.4k • written 4.3 years ago by • 0
0
votes
0
replies
1.0k
views
getGFFSet function CRASHES R session
getGFF NCBI biomartr biomaRt
4.3 years ago Matan G. ▴ 60
2
votes
6
replies
2.1k
views
Biomart's getBM returns no genes for an existing GO-term in grch38, and less then expected in grch37
GO biomaRt
updated 4.3 years ago by ★ 6.6k • written 4.3 years ago by • 0
1
vote
2
replies
1.8k
views
What are these genes ? [How to get Ensembl IDs for them]
AnnotationDbi biomaRt
updated 4.4 years ago by ▴ 30 • written 4.4 years ago by • 0
0
votes
6
replies
2.8k
views
Getting paralogus genes from biomart for mouse
biomart biomaRt Ensembl
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
2
votes
8
replies
3.3k
views
error in getBM (biomaRt): "error: no such table: metadata"
biomaRt software error
updated 4.4 years ago by ★ 6.6k • written 5.5 years ago by • 0
1
vote
7
replies
6.1k
views
Using R BioMart getting orthologus genes between two species
biomaRt
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
0
votes
3
replies
2.4k
views
How to correlate bp and Chr columns in the corresponding RSID column?
biomaRt
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
0
votes
2
replies
1.5k
views
Can't retrieve upstream flank (biomaRt)
biomaRt
4.4 years ago Pete • 0
5
votes
5
replies
6.4k
views
BiomaRt connection error: Could not connect to mysql database ensembl_mart_104
biomaRt connection sql
updated 4.5 years ago by ▴ 80 • written 4.5 years ago by ▴ 10
0
votes
1
reply
1.1k
views
biomaRt - rice genes database not working
biomaRt
updated 4.5 years ago by ★ 1.4k • written 4.5 years ago by • 0
4
votes
9
replies
4.8k
views
biomaRt - getBM; Error with obtaining a dataset from getBM() function
biomaRt error getBM
updated 4.5 years ago by ★ 6.6k • written 4.8 years ago by ▴ 20
6
votes
6
replies
3.6k
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
4.6 years ago svlachavas ▴ 840
1
vote
0
replies
1.5k
views
News: Ensembl 104 has just been released!
ensembldb biomaRt
4.6 years ago mchakiachvili ▴ 20
2
votes
6
replies
2.4k
views
BiomaRt getBM Error when converting from Ensemble to RNACentral IDs
biomaRt
written 4.6 years ago by • 0
2
votes
3
replies
2.3k
views
Ensemble site connection error
biomaRt
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by ▴ 10
4
votes
2
replies
1.4k
views
Biomart Errors
biomaRt
4.6 years ago Dr. Connie Brett ▴ 20
1
vote
2
replies
3.1k
views
BiomaRt conversion
biomaRt
4.7 years ago gwendal.lazennec • 0
2
votes
1
reply
2.9k
views
Retrieve gene description with ensembldb
biomaRt ensembldb AnnotationData
updated 4.7 years ago by ★ 2.1k • written 4.7 years ago by ▴ 510
0
votes
3
replies
6.9k
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub biomaRt
updated 3.3 years ago by • 0 • written 4.7 years ago by ▴ 20
1,083 results • Page 3 of 22
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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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