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488
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How to count mutations to check for transcription strand bias?
strand transcription bias mutations counting
2.4 years ago by n,n ▴ 370
0
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1
reply
912
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Answer: Answer: The best single metric for a correlation matrix
3.0 years ago by n,n ▴ 370
0
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0
replies
687
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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
3.0 years ago by n,n ▴ 370
9
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10
replies
5.9k
views
What exactly should and shouldn't go in Combat's model matrix?
batch effects expression gene combat
updated 3.4 years ago by ★ 3.0k • written 3.5 years ago by ▴ 370
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1
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5.9k
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Answer: Answer: What exactly should and shouldn't go in Combat's model matrix?
3.4 years ago by n,n ▴ 370
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0
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5.9k
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Comment: Comment: What exactly should and shouldn't go in Combat's model matrix?
3.4 years ago by n,n ▴ 370
0
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1
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5.9k
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Comment: Comment: What exactly should and shouldn't go in Combat's model matrix?
3.5 years ago by n,n ▴ 370
1
vote
0
replies
674
views
Does the GAF gene ontologies file only contain terms that are leaf nodes?
gene GO ontology
3.5 years ago by n,n ▴ 370
0
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1
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1.8k
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Comment: Comment: How to cite a pathway from wikipathways in text and in references in APA format
3.5 years ago by n,n ▴ 370
2
votes
2
replies
1.0k
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Will quantile normalization affect the result of the Tau statistic?
RNA-Seq tissue-specificity tau
3.9 years ago by n,n ▴ 370
0
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0
replies
653
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Documentation on the contents of the "pubtatordb" package in R?
R pubtator
4.0 years ago by n,n ▴ 370
5
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8
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4.4k
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Filtering contigs by length during assembly?
Assembly
updated 4.2 years ago by 20 • written 6.2 years ago by ▴ 370
1
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7
replies
2.2k
views
Error using the getGEO() patcher
GEOQuery R Bioconductor
updated 4.5 years ago by 20 • written 4.7 years ago by ▴ 370
0
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1
reply
1.5k
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Comment: C: Interpretation of "standardized expression matrix"?
4.5 years ago by n,n ▴ 370
0
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0
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1.5k
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Comment: C: Interpretation of "standardized expression matrix"?
4.5 years ago by n,n ▴ 370
0
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2
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1.5k
views
Comment: C: Interpretation of "standardized expression matrix"?
4.5 years ago by n,n ▴ 370
2
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6
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1.5k
views
Interpretation of "standardized expression matrix"?
RNA-Seq normalization
updated 4.5 years ago by 88k • written 4.5 years ago by ▴ 370
11
votes
1
reply
6.8k
views
How to interpret "pseudo count" in gene expression data handling context?
RNA-Seq normalization
updated 4.6 years ago by 85k • written 4.6 years ago by ▴ 370
0
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1
reply
2.2k
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Comment: C: Error using the getGEO() patcher
4.7 years ago by n,n ▴ 370
0
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1
reply
2.2k
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Comment: C: Error using the getGEO() patcher
4.7 years ago by n,n ▴ 370
0
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1
reply
2.2k
views
Comment: C: Error using the getGEO() patcher
4.7 years ago by n,n ▴ 370
3
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3
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3.3k
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What are some references of works that use a TPM expression threshold for filtering samples/genes?
RNA-Seq
updated 4.7 years ago by 20 • written 4.8 years ago by ▴ 370
3
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1
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1.4k
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Answer: A: Correlation vs differential expression testing
4.8 years ago by n,n ▴ 370
0
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0
replies
1.3k
views
Extra adjustment variables during batch effect correction
rna-seq ComBat batch-effect
updated 7 months ago by 44k • written 4.9 years ago by ▴ 370
0
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1
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1.5k
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Comment: C: statistics method to find the relation between multiple variables of 50 samples
4.9 years ago by n,n ▴ 370
1
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1
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1.2k
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Comment: C: Can I use batch effect correction "by parts"?
4.9 years ago by n,n ▴ 370
0
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1
reply
1.2k
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Comment: C: Can I use batch effect correction "by parts"?
4.9 years ago by n,n ▴ 370
0
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1
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1.2k
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Comment: C: Can I use batch effect correction "by parts"?
4.9 years ago by n,n ▴ 370
3
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7
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1.2k
views
Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 7 months ago by 44k • written 4.9 years ago by ▴ 370
0
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0
replies
912
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Comment: C: Time Series Network Identification (TSNI) data scaling
4.9 years ago by n,n ▴ 370
0
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2
replies
912
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Time Series Network Identification (TSNI) data scaling
expression TSNI
updated 4.9 years ago by ▴ 140 • written 4.9 years ago by ▴ 370
0
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1
reply
2.6k
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Comment: C: Should normalization of expression data be performed over the entire dataset or
5.0 years ago by n,n ▴ 370
4
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4
replies
2.6k
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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 5.0 years ago by ★ 7.6k • written 5.0 years ago by ▴ 370
0
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0
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4.6k
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Comment: C: Transcript vs. Gene TPM counts?
5.0 years ago by n,n ▴ 370
11
votes
7
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4.6k
views
Transcript vs. Gene TPM counts?
RNA-Seq GTEx GTEX
updated 5.1 years ago by ★ 4.1k • written 5.1 years ago by ▴ 370
0
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2
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4.6k
views
Comment: C: Transcript vs. Gene TPM counts?
5.1 years ago by n,n ▴ 370
0
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0
replies
789
views
How to efficiently fetch methylation beta values across multiple genes for multiple samples?
mehtylation database
5.3 years ago by n,n ▴ 370
1
vote
1
reply
1.1k
views
Download tissue distribution data from COSMIC?
database cosmic
updated 5.5 years ago by 20 • written 5.7 years ago by ▴ 370
0
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0
replies
999
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Comment: C: basic command in bash
6.0 years ago by n,n ▴ 370
0
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0
replies
2.5k
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Answer: A: blastp download option with csv
6.0 years ago by n,n ▴ 370
0
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1
reply
2.2k
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Comment: C: Extract sequences from the raw reads
6.1 years ago by n,n ▴ 370
3
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0
replies
1.8k
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Answer: A: counting number of genes located on positive or negative strands
6.1 years ago by n,n ▴ 370
1
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1
reply
1.3k
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Answer: A: need code for sorting fasta header
6.1 years ago by n,n ▴ 370
2
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1
reply
2.1k
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Answer: A: How to separate mixed orientation raw illumina sequence into forward and reverse
6.1 years ago by n,n ▴ 370
0
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0
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1.9k
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Comment: C: Faster way to get sequences from large fasta files?
6.1 years ago by n,n ▴ 370
1
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1
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1.9k
views
Answer: A: Faster way to get sequences from large fasta files?
6.1 years ago by n,n ▴ 370
0
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0
replies
1.1k
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Comment: C: gene expression for cancer identification
6.1 years ago by n,n ▴ 370
3
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0
replies
2.4k
views
Answer: A: manipulating a file by R or bash?
6.1 years ago by n,n ▴ 370
1
vote
2
replies
5.6k
views
Answer: A: Join/Combine gff3 or gtf files
6.1 years ago by n,n ▴ 370
1
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1
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1.7k
views
Answer: A: How to write a proper bed file to extract sequence?
6.1 years ago by n,n ▴ 370
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