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3
votes
14
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4.7k
views
biomaRt - Error in getBM: The query to the BioMart webservice returned an invalid result
biomart error ensembl bioconductor ensembl mart
8.3 years ago daniel.carbajo • 0
1
vote
0
replies
1.5k
views
News: Ensembl 89 has been released
ensembl biomart ensemblbiomart ensembl89 News
8.3 years ago Thomas Maurel ▴ 800
0
votes
3
replies
1.5k
views
DESeq2 output with multiple Ensembl Gene Names per row, how to resolve?
rnaseq deseq2 ensembl
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
2
votes
12
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3.6k
views
biomaRt does not return entrezgene id
bioconductor biomart entrez gene identifiers ensembl ensembl mart
updated 8.4 years ago by ▴ 800 • written 8.4 years ago by • 0
5
votes
5
replies
2.7k
views
News: Ensembl 88 is out!
ensembl ensembl mart biomart e!88 News
8.5 years ago Thomas Maurel ▴ 800
0
votes
0
replies
1.3k
views
News: Ensembl 87 is out!
ensembl ensemble mart ensembl mart biomart News
8.8 years ago amonida ▴ 20
1
vote
1
reply
1.5k
views
News: Ensembl release 86 is out!
ensembl biomart ensembl release ensembl mart News
8.9 years ago Thomas Maurel ▴ 800
0
votes
2
replies
2.3k
views
Gviz - adding ensembl gene annotation track
gviz ensembl
9.0 years ago just • 0
0
votes
5
replies
2.0k
views
Using mgeneSim with Ensembl ids
Ensembl GOsemsim GO semantic similarity
updated 9.0 years ago by ★ 1.2k • written 9.0 years ago by ▴ 10
1
vote
0
replies
1.5k
views
News: Ensembl release 85 is out!
ensembl biomart release85 ensembl release mart News
9.1 years ago Thomas Maurel ▴ 800
0
votes
5
replies
5.7k
views
Ensembl biomaRt connection errors
software error biomart ensembl
updated 9.2 years ago by ▴ 70 • written 9.2 years ago by • 0
1
vote
5
replies
3.7k
views
Ensembl bacteria not accessible from biomaRt
biomart ensembl
updated 9.3 years ago by 25k • written 9.3 years ago by ▴ 20
0
votes
1
reply
1.2k
views
Ensembl version from non-vertebrate biomaRt
biomart ensembl
updated 9.3 years ago by ▴ 70 • written 9.3 years ago by ▴ 20
4
votes
9
replies
3.7k
views
News: Ensembl release 84 is out!
ensembl mart release84 biomart ensembl release News
updated 9.4 years ago by ▴ 20 • written 9.5 years ago by ▴ 800
2
votes
2
replies
1.4k
views
goseq package: Is the package in sync with the most current Ensembl release?
goseq ensembl
updated 9.4 years ago by ★ 2.1k • written 9.4 years ago by ▴ 10
0
votes
0
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1.4k
views
Low yield mapping ensembl transcript ids to entrez gene ids in biomart
biomart ensembl ensemble mart entrez gene identifiers
9.6 years ago serpalma.v ▴ 60
4
votes
5
replies
2.1k
views
ChIPpeakAnno getAnnotation request fail
chippeakanno biomart ensembl
9.7 years ago igor ▴ 50
0
votes
0
replies
1.9k
views
News: Ensembl 83 is out!
ensemble mart ensembl biomart ensembl release News
9.8 years ago amonida ▴ 20
1
vote
2
replies
4.1k
views
Converting annotation from UCSC to Ensembl
ensembl ucsc annotation
updated 9.8 years ago by 68k • written 9.8 years ago by ▴ 110
0
votes
0
replies
1.8k
views
News: Ensembl GRCh37 release 82 - second data update
ensembl biomart News grch37 GRCh37
9.9 years ago amonida ▴ 20
0
votes
0
replies
1.4k
views
News: Ensembl release 82 is out!
biomart ensembl release82 variation mouse News
10.0 years ago Thomas Maurel ▴ 800
0
votes
3
replies
3.0k
views
biomaRt fails for M.musculus annotation, Ensembl version 80
biomart ensembl
updated 10.0 years ago by ▴ 20 • written 10.0 years ago by ▴ 80
0
votes
1
reply
2.0k
views
Problem with visualising empty tracks from ensembl
gviz ensembl
updated 10.0 years ago by ★ 1.6k • written 10.1 years ago by • 0
1
vote
2
replies
1.4k
views
Using Ensmbl rel 80, when rel 79 is supported by BioConductor
ensembl
updated 10.1 years ago by ★ 2.1k • written 10.1 years ago by • 0
5
votes
2
replies
3.3k
views
News: Ensembl release 81 is out!
human mouse GRCh38 biomart Ensembl News
updated 10.2 years ago by ▴ 390 • written 10.2 years ago by ▴ 800
2
votes
4
replies
2.1k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl macaque dbsnp customprodb
updated 10.2 years ago by ▴ 50 • written 10.2 years ago by • 0
0
votes
2
replies
1.9k
views
Ensembl database query with biomart behaves strangely when using chromosomes as filter values
biomart ensembl
updated 10.2 years ago by ▴ 800 • written 10.2 years ago by ▴ 20
2
votes
1
reply
1.4k
views
Why does biomaRt query show inconsistent behavior with ensembl versions from March and May
biomart ensembl
10.2 years ago jmeisig ▴ 20
2
votes
1
reply
1.4k
views
GoSeq: use ENSEMBLTRANS as input
goseq ensembl
updated 10.3 years ago by ▴ 320 • written 10.3 years ago by ▴ 10
9
votes
1
reply
2.7k
views
News: Ensembl release 80 is out!
biomart Ensembl zebrafish Rat 1000 genomes phase 3 News
updated 10.3 years ago by ▴ 390 • written 10.3 years ago by ▴ 800
0
votes
0
replies
1.9k
views
News: Ensembl GRCh37 release 79 data update
biomart ensembl release news GRCh37 News
10.5 years ago Thomas Maurel ▴ 800
0
votes
5
replies
2.2k
views
News: Ensembl 79 release is out!
Ensembl biomart release news News
updated 10.5 years ago by ★ 8.2k • written 10.5 years ago by ▴ 20
0
votes
6
replies
2.9k
views
converting UniProt to SGD ids using UniProt.wd
uniprot.ws uniprot ensembl
updated 10.7 years ago by ★ 7.2k • written 10.7 years ago by ▴ 160
0
votes
2
replies
2.6k
views
use BiomartGeneRegionTrack with the dataset grch37.ensembl.org
gviz ensembl biomart
10.7 years ago Tiphaine Martin ▴ 40
0
votes
2
replies
2.0k
views
Missing ensembl_ids in biomaRt uniprot query
biomaRt uniprot ensembl
updated 10.8 years ago by • 0 • written 10.8 years ago by ▴ 510
0
votes
0
replies
1.5k
views
News: Ensembl 78 release is out!
Ensembl Biomart News
10.8 years ago amonida ▴ 20
6
votes
5
replies
8.8k
views
biomaRt: no access to Ensembl_75 (GRCh37.p13)
biomarRt ensembl
updated 10.8 years ago by • 0 • written 10.9 years ago by • 0
2
votes
3
replies
12k
views
BiomaRt: protein coding transcript identification
ensembl protein coding biomart
updated 10.9 years ago by ▴ 800 • written 10.9 years ago by ▴ 120
13
votes
8
replies
18k
views
how to use biomaRt with ensembl build 37
biomaRt ensembl GRCh37
updated 10.9 years ago by ▴ 800 • written 10.9 years ago by ▴ 90
0
votes
0
replies
1.7k
views
News: Useful information about Ensembl release 77 mart databases
ensembl biomart Vervet-AGM News
10.9 years ago Thomas Maurel ▴ 800
140 results • Page 3 of 3
Recent ...
Replies
Comment: 3-factor DESeq2 trime-series analysis by swbarnes2 ★ 1.4k
What does your PCA look like? A lot of times, I find that different cell lines are so different from each other, that they should not be d…
Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by yongjie.wang • 0
Thanks for your reply. " normFactors <- exp(-1 * offst(set2)) normFactors <- normFactors / exp(rowMeans(log(normFactors))) normalizat…
Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …
Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k
> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…
Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
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Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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