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0
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0
replies
380
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How to count mutations to check for transcription strand bias?
strand transcription bias mutations counting
22 months ago by n,n ▴ 360
0
votes
0
replies
605
views
Why can I not reproduce some of TCGA's MAF file contexts from the coding sequences of the mutated genes?
context MAF TCGA CDS
2.5 years ago by n,n ▴ 360
9
votes
10
replies
5.0k
views
What exactly should and shouldn't go in Combat's model matrix?
batch effects expression gene combat
updated 2.9 years ago by ★ 2.9k • written 2.9 years ago by ▴ 360
1
vote
0
replies
607
views
Does the GAF gene ontologies file only contain terms that are leaf nodes?
gene GO ontology
2.9 years ago by n,n ▴ 360
2
votes
2
replies
900
views
Will quantile normalization affect the result of the Tau statistic?
RNA-Seq tissue-specificity tau
3.3 years ago by n,n ▴ 360
0
votes
0
replies
595
views
Documentation on the contents of the "pubtatordb" package in R?
R pubtator
3.5 years ago by n,n ▴ 360
5
votes
8
replies
3.9k
views
Filtering contigs by length during assembly?
Assembly
updated 3.6 years ago by 20 • written 5.6 years ago by ▴ 360
1
vote
7
replies
2.0k
views
Error using the getGEO() patcher
GEOQuery R Bioconductor
updated 3.9 years ago by 20 • written 4.1 years ago by ▴ 360
2
votes
6
replies
1.3k
views
Interpretation of "standardized expression matrix"?
RNA-Seq normalization
updated 4.0 years ago by 87k • written 4.0 years ago by ▴ 360
10
votes
1
reply
6.1k
views
How to interpret "pseudo count" in gene expression data handling context?
RNA-Seq normalization
updated 4.0 years ago by 82k • written 4.0 years ago by ▴ 360
3
votes
3
replies
2.9k
views
What are some references of works that use a TPM expression threshold for filtering samples/genes?
RNA-Seq
updated 4.2 years ago by 20 • written 4.2 years ago by ▴ 360
0
votes
0
replies
1.2k
views
Extra adjustment variables during batch effect correction
rna-seq ComBat batch-effect
updated 18 days ago by 43k • written 4.3 years ago by ▴ 360
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 17 days ago by 43k • written 4.3 years ago by ▴ 360
0
votes
2
replies
792
views
Time Series Network Identification (TSNI) data scaling
expression TSNI
updated 4.3 years ago by ▴ 140 • written 4.3 years ago by ▴ 360
4
votes
4
replies
2.3k
views
Should normalization of expression data be performed over the entire dataset or only over the used subset of data?
RNA-Seq quantile normalization co-expression
updated 4.4 years ago by ★ 7.1k • written 4.4 years ago by ▴ 360
11
votes
7
replies
4.0k
views
Transcript vs. Gene TPM counts?
RNA-Seq GTEx GTEX
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by ▴ 360
0
votes
0
replies
739
views
How to efficiently fetch methylation beta values across multiple genes for multiple samples?
mehtylation database
4.8 years ago by n,n ▴ 360
1
vote
1
reply
1.0k
views
Download tissue distribution data from COSMIC?
database cosmic
updated 5.0 years ago by 20 • written 5.1 years ago by ▴ 360
1
vote
2
replies
843
views
RefSeq IDs question
sequence
5.6 years ago by n,n ▴ 360
0
votes
0
replies
850
views
Bugged Velveth AMOS (.afg) file?
Assembly
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 360
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