Showing : BioMart • reset
21
votes
14
replies
1.2k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 11 days ago by • 0 • written 5 weeks ago by ▴ 50
21
votes
34
replies
4.9k
views
Biomart error when updating to R 4.0.2
Biomart
updated 19 months ago by ★ 5.5k • written 19 months ago by ▴ 40
21
votes
24
replies
10.0k
views
Problem with biomart's listMarts function
biomart bug
updated 6.0 years ago by ▴ 470 • written 6.5 years ago by ★ 1.9k
19
votes
4
replies
4.6k
views
biomaRt no longer works with proxy after upgrade
biomart proxy rcurl
updated 6.5 years ago by ▴ 140 • written 6.5 years ago by ▴ 610
13
votes
8
replies
13k
views
how to use biomaRt with ensembl build 37
biomaRt ensembl GRCh37
updated 7.6 years ago by ▴ 790 • written 7.6 years ago by ▴ 90
11
votes
5
replies
3.1k
views
Scan error using biomart with version option
biomart
updated 4.3 years ago by ★ 5.5k • written 4.4 years ago by ▴ 40
10
votes
8
replies
1.3k
views
Best alternative annotation package to BiomaRt
R biomaRt Ensembl rnaseq
2.9 years ago m93 ▴ 10
9
votes
4
replies
3.7k
views
How to access Emsembl plants with biomaRt
biomart
6.5 years ago naholi.alejandri ▴ 50
9
votes
9
replies
2.8k
views
biomaRt error when connecting to host
biomart host connection
updated 5.1 years ago by ★ 5.5k • written 5.1 years ago by ★ 1.5k
9
votes
5
replies
4.7k
views
Error: This function only works when used with the ensembl BioMart.
biomart error
6.5 years ago anchel.gonzalez • 0
9
votes
1
reply
1.7k
views
News: Ensembl release 80 is out!
biomart Ensembl zebrafish Rat 1000 genomes phase 3 News
updated 7.0 years ago by ▴ 380 • written 7.0 years ago by ▴ 790
8
votes
8
replies
1.7k
views
biomaRt: drerio_gene_ensembl dataset missing
biomart ensembl ripseeker
updated 4.4 years ago by ★ 5.5k • written 4.4 years ago by ▴ 480
8
votes
10
replies
782
views
Genes listed in GO categories
goseq biomart
updated 3.9 years ago by 45k • written 3.9 years ago by • 0
8
votes
6
replies
1.5k
views
Coding vs Noncoding Genes in Hit List
biomaRt coding vs noncoding high throughput
updated 2.7 years ago by 25k • written 2.7 years ago by ▴ 10
7
votes
2
replies
5.1k
views
getBM error: The query to the BioMart webservice returned an invalid result
biomart
updated 4.3 years ago by ★ 5.5k • written 4.3 years ago by ▴ 30
6
votes
12
replies
3.6k
views
Error in getBM of biomaRt package
biomaRt getBM
updated 5.1 years ago by • 0 • written 5.3 years ago by ▴ 100
6
votes
6
replies
1.3k
views
GenomicFeatures makeTxDbFromBiomart fails with "unkown species" error
biomart maketxdbfrombiomart genomicfeatures
updated 5.3 years ago by 59k • written 5.3 years ago by ▴ 30
6
votes
5
replies
1.2k
views
biomaRt returns all NAs for hgnc_symbol
biomaRt
updated 3.1 years ago by ★ 5.5k • written 3.1 years ago by ▴ 80
6
votes
5
replies
2.6k
views
biomaRt Ensembl gene ID to multiple HGNC symbol
ensembl symbol hgnc biomart
updated 3.0 years ago by 59k • written 3.0 years ago by ▴ 80
6
votes
7
replies
1.3k
views
Inconsistencies in biomart results
biomart
updated 5.0 years ago by ★ 5.5k • written 5.7 years ago by 1.5k
6
votes
2
replies
2.3k
views
The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in …
biomart number of columns in the result table does not equal the number of attributes in the query
updated 4.4 years ago by ▴ 160 • written 4.4 years ago by ▴ 20
6
votes
1
reply
2.5k
views
[ReportingTools] HTMLReport of DESeq2 results using Ensembl Gene Ids
Sequencing Annotation convert biomaRt ReportingTools DESeq2 Sequencing Annotation convert
updated 7.4 years ago by ▴ 360 • written 8.4 years ago by ▴ 160
6
votes
1
reply
634
views
biomart R code cannot retrieve gene symbol
biomart ensemblbiomart ensemble mart
4.1 years ago emmak ▴ 20
6
votes
7
replies
4.4k
views
BiomaRt workaround when Biomart server closed
biomart
updated 6.5 years ago by • 0 • written 6.5 years ago by ▴ 30
6
votes
5
replies
6.4k
views
biomaRt: error using useDataset or useMart
software error biomart usemart usedataset
updated 4.4 years ago by ★ 5.5k • written 4.4 years ago by ▴ 40
6
votes
18
replies
2.3k
views
biomaRt - getBM - biomart= ENSEMBL_MART_FUNCGEN !!! NOT WORKING!!!
bioconductor biomart problem with connection
updated 5.9 years ago by ▴ 70 • written 5.9 years ago by ▴ 10
6
votes
6
replies
726
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
12 months ago svlachavas ▴ 780
5
votes
4
replies
2.0k
views
biomaRT GO-ID retreival showing different genes than AmiGO
biomart go
updated 5.4 years ago by ★ 5.5k • written 5.4 years ago by ▴ 40
5
votes
3
replies
2.3k
views
Please use the function 'listAttributes' to get valid attribute names
r biomart
4.8 years ago al14 • 0
5
votes
2
replies
1.8k
views
News: Ensembl release 81 is out!
human mouse GRCh38 biomart Ensembl News
updated 6.8 years ago by ▴ 380 • written 6.8 years ago by ▴ 790
5
votes
19
replies
5.9k
views
biomaRt SNP (rs ID) -to-HGNC symbol mapping question
biomart
7.6 years ago k.askland ▴ 20
5
votes
5
replies
1.2k
views
News: Ensembl 88 is out!
ensembl ensembl mart biomart e!88 News
5.1 years ago Thomas Maurel ▴ 790
5
votes
2
replies
8.5k
views
Probe to gene id conversion
annotate biomart probe to gene id
updated 7.6 years ago by 59k • written 7.6 years ago by ▴ 20
5
votes
11
replies
748
views
"associated_gene" attribute from biomaRt returns too few values - SNP(rsID dataset)
r biomart SNP annotation HUGO
updated 21 months ago by ★ 5.5k • written 21 months ago by • 0
5
votes
5
replies
1.4k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
7.7 years ago patrick.schordert ▴ 30
5
votes
5
replies
2.8k
views
SNP Function Information from biomaRt
biomart snp nonsynonymous
updated 7.6 years ago by 21k • written 7.6 years ago by ▴ 10
5
votes
4
replies
974
views
Biomart: Error in getLDS
Biomart
updated 5.5 years ago by 59k • written 5.5 years ago by ▴ 10
5
votes
7
replies
1.9k
views
Biomart getLDS error
biomart getLDS orthlog
updated 5.6 years ago by ▴ 790 • written 5.6 years ago by • 0
5
votes
6
replies
1.5k
views
Reactome pathway names from IDs?
biomart reactome reactome.db id
updated 6.5 years ago by 59k • written 6.5 years ago by ▴ 610
5
votes
16
replies
2.4k
views
biomaRt error in getBM for hsapiens_gene_ensembl
biomart
updated 4.4 years ago by • 0 • written 4.4 years ago by ▴ 20
5
votes
11
replies
870
views
an error in BioMart regarding gene annotations
biomart AnnotationDbi
updated 3.9 years ago by ▴ 50 • written 3.9 years ago by ▴ 640
4
votes
9
replies
2.0k
views
News: Ensembl release 84 is out!
ensembl mart release84 biomart ensembl release News
updated 6.1 years ago by ▴ 20 • written 6.2 years ago by ▴ 790
4
votes
7
replies
1.9k
views
How to get Genomic feature in txdb format from biomart for sacCer2 (EF4) assembly?
makeTxDbFromBiomart genomicfeatures txdb biomart
updated 6.6 years ago by 59k • written 6.6 years ago by ▴ 50
4
votes
5
replies
1.4k
views
biomaRt error: Query ERROR: caught BioMart::Exception: non-BioMart die():
biomart
4.6 years ago • updated 4.5 years ago Georg Otto ▴ 120
4
votes
1
reply
1.1k
views
Retrieving all genes related a go term
go R annotationdbi biomart
updated 4.7 years ago by 59k • written 4.7 years ago by ▴ 40
4
votes
3
replies
2.2k
views
'biomaRt expected a character string of length 1' error with getBM and reseq mrna filer
biomart
updated 3.0 years ago by ★ 5.5k • written 3.0 years ago by • 0
4
votes
2
replies
715
views
bioMart error - The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1
biomaRt
updated 2.9 years ago by ★ 5.5k • written 2.9 years ago by ▴ 50
4
votes
5
replies
1.4k
views
How can I use biomaRt on previus databases?
biomart previus database retrive sequence
7.0 years ago kris.petrini • 0
4
votes
7
replies
1.1k
views
Requesting flank sequences (BioMart::Exception)
biomart plants_mart
updated 15 months ago by ▴ 20 • written 6.0 years ago by • 0
4
votes
4
replies
2.0k
views
Mouse genes not mapping to Human orthologs
biomaRt
3.0 years ago komal.rathi ▴ 100
50 results • Page 1 of 1
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Comment: featureCounts: 0% successfully assigned fragments by KMS • 0
Dear ATpoint I am exactly looking for read/gene count from BAM/SAM file either through ht-seq or feature count feature count giving me 0% s…
Answer: Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene by James W. MacDonald 59k
There is the ncbiRefSeqSelect table that has the MANE and RefSeq Select transcripts. It's not just the MANE though. ``` > z <- makeTxDb…
Comment: Handling of missing values in limma by AyHi • 0
Thank you, Gordon, for your reply. I used sum(is.na(lmfit)) after lmFit, but somewhat it indicated there was no NA observations even when…
Comment: merging VCF files by lesefo6448 • 0
You can use this VCF Merger Software if you want to Merge VCF files into one file. this Software easily Merge your multiple VCF files with…
Comment: featureCounts: 0% successfully assigned fragments by ATpoint ★ 1.2k
What you have to do is to check whether the chromosome names in the BAM file are part of the GTF. Do it programatically, not by eye. Extrac…
Votes
Answer: Load packages when using BatchtoolsParam
Comment: Load packages when using BatchtoolsParam
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
A: DESeq2: thousands of NA for pvalues?
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Scholar to James W. MacDonald 59k
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