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675
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How to count mutations to check for transcription strand bias?
strand transcription bias mutations counting
3.2 years ago by n,n ▴ 390
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1
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1.2k
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Answer: Answer: The best single metric for a correlation matrix
3.9 years ago by n,n ▴ 390
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0
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907
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Why can I not reproduce some of TCGA's MAF file contexts from the coding sequences of the mutated genes?
context MAF TCGA CDS
3.9 years ago by n,n ▴ 390
11
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10
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9.0k
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What exactly should and shouldn't go in Combat's model matrix?
batch effects expression gene combat
updated 4.3 years ago by ★ 3.1k • written 4.3 years ago by ▴ 390
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9.0k
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Answer: Answer: What exactly should and shouldn't go in Combat's model matrix?
4.3 years ago by n,n ▴ 390
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0
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9.0k
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Comment: Comment: What exactly should and shouldn't go in Combat's model matrix?
4.3 years ago by n,n ▴ 390
0
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1
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9.0k
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Comment: Comment: What exactly should and shouldn't go in Combat's model matrix?
4.3 years ago by n,n ▴ 390
1
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0
replies
810
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Does the GAF gene ontologies file only contain terms that are leaf nodes?
gene GO ontology
4.3 years ago by n,n ▴ 390
0
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1
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2.6k
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Comment: Comment: How to cite a pathway from wikipathways in text and in references in APA format
4.3 years ago by n,n ▴ 390
2
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2
replies
1.3k
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Will quantile normalization affect the result of the Tau statistic?
RNA-Seq tissue-specificity tau
4.7 years ago by n,n ▴ 390
0
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0
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784
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Documentation on the contents of the "pubtatordb" package in R?
R pubtator
4.9 years ago by n,n ▴ 390
5
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8
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5.1k
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Filtering contigs by length during assembly?
Assembly
updated 5.0 years ago by 20 • written 7.0 years ago by ▴ 390
1
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7
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2.7k
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Error using the getGEO() patcher
GEOQuery R Bioconductor
updated 5.3 years ago by 20 • written 5.5 years ago by ▴ 390
0
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1
reply
2.1k
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Comment: C: Interpretation of "standardized expression matrix"?
5.4 years ago by n,n ▴ 390
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0
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2.1k
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Comment: C: Interpretation of "standardized expression matrix"?
5.4 years ago by n,n ▴ 390
0
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2
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2.1k
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Comment: C: Interpretation of "standardized expression matrix"?
5.4 years ago by n,n ▴ 390
2
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6
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2.1k
views
Interpretation of "standardized expression matrix"?
RNA-Seq normalization
updated 5.4 years ago by 89k • written 5.4 years ago by ▴ 390
11
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1
reply
7.6k
views
How to interpret "pseudo count" in gene expression data handling context?
RNA-Seq normalization
updated 5.4 years ago by 89k • written 5.4 years ago by ▴ 390
0
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1
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2.7k
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Comment: C: Error using the getGEO() patcher
5.5 years ago by n,n ▴ 390
0
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1
reply
2.7k
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Comment: C: Error using the getGEO() patcher
5.5 years ago by n,n ▴ 390
0
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1
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2.7k
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Comment: C: Error using the getGEO() patcher
5.5 years ago by n,n ▴ 390
3
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3
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4.4k
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What are some references of works that use a TPM expression threshold for filtering samples/genes?
RNA-Seq
updated 5.6 years ago by 20 • written 5.6 years ago by ▴ 390
3
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1
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2.0k
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Answer: A: Correlation vs differential expression testing
5.6 years ago by n,n ▴ 390
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0
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1.5k
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Extra adjustment variables during batch effect correction
rna-seq ComBat batch-effect
updated 17 months ago by 45k • written 5.7 years ago by ▴ 390
0
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1
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2.0k
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Comment: C: statistics method to find the relation between multiple variables of 50 samples
5.7 years ago by n,n ▴ 390
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1
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1.7k
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Comment: C: Can I use batch effect correction "by parts"?
5.7 years ago by n,n ▴ 390
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1
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1.7k
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Comment: C: Can I use batch effect correction "by parts"?
5.7 years ago by n,n ▴ 390
0
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1
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1.7k
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Comment: C: Can I use batch effect correction "by parts"?
5.7 years ago by n,n ▴ 390
3
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7
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1.7k
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Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 17 months ago by 45k • written 5.7 years ago by ▴ 390
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0
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1.2k
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Comment: C: Time Series Network Identification (TSNI) data scaling
5.7 years ago by n,n ▴ 390
0
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2
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1.2k
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Time Series Network Identification (TSNI) data scaling
expression TSNI
updated 5.7 years ago by ▴ 140 • written 5.7 years ago by ▴ 390
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1
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3.3k
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Comment: C: Should normalization of expression data be performed over the entire dataset or
5.8 years ago by n,n ▴ 390
4
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4
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3.3k
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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 5.8 years ago by ★ 8.3k • written 5.8 years ago by ▴ 390
0
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0
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5.7k
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Comment: C: Transcript vs. Gene TPM counts?
5.8 years ago by n,n ▴ 390
11
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7
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5.7k
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Transcript vs. Gene TPM counts?
RNA-Seq GTEx GTEX
updated 6.0 years ago by ★ 4.2k • written 6.0 years ago by ▴ 390
0
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2
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5.7k
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Comment: C: Transcript vs. Gene TPM counts?
6.0 years ago by n,n ▴ 390
0
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0
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899
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How to efficiently fetch methylation beta values across multiple genes for multiple samples?
mehtylation database
6.2 years ago by n,n ▴ 390
1
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1
reply
1.3k
views
Download tissue distribution data from COSMIC?
database cosmic
updated 6.4 years ago by 20 • written 6.5 years ago by ▴ 390
0
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0
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1.2k
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Comment: C: basic command in bash
6.9 years ago by n,n ▴ 390
0
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0
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2.7k
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Answer: A: blastp download option with csv
6.9 years ago by n,n ▴ 390
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1
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2.6k
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Comment: C: Extract sequences from the raw reads
6.9 years ago by n,n ▴ 390
3
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0
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2.2k
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Answer: A: counting number of genes located on positive or negative strands
6.9 years ago by n,n ▴ 390
1
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1
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1.7k
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Answer: A: need code for sorting fasta header
6.9 years ago by n,n ▴ 390
2
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1
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2.4k
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Answer: A: How to separate mixed orientation raw illumina sequence into forward and reverse
6.9 years ago by n,n ▴ 390
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0
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2.5k
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Comment: C: Faster way to get sequences from large fasta files?
6.9 years ago by n,n ▴ 390
1
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1
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2.5k
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Answer: A: Faster way to get sequences from large fasta files?
6.9 years ago by n,n ▴ 390
0
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0
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1.4k
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Comment: C: gene expression for cancer identification
6.9 years ago by n,n ▴ 390
3
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0
replies
3.2k
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Answer: A: manipulating a file by R or bash?
7.0 years ago by n,n ▴ 390
1
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2
replies
6.2k
views
Answer: A: Join/Combine gff3 or gtf files
7.0 years ago by n,n ▴ 390
1
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1
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1.9k
views
Answer: A: How to write a proper bed file to extract sequence?
7.0 years ago by n,n ▴ 390
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