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375
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How to count mutations to check for transcription strand bias?
strand transcription bias mutations counting
21 months ago by n,n ▴ 360
0
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1
reply
812
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Answer: Answer: The best single metric for a correlation matrix
2.5 years ago by n,n ▴ 360
0
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0
replies
604
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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
2.5 years ago by n,n ▴ 360
9
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10
replies
4.9k
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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
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1
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4.9k
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Answer: Answer: What exactly should and shouldn't go in Combat's model matrix?
2.9 years ago by n,n ▴ 360
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0
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4.9k
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Comment: Comment: What exactly should and shouldn't go in Combat's model matrix?
2.9 years ago by n,n ▴ 360
0
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1
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4.9k
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Comment: Comment: What exactly should and shouldn't go in Combat's model matrix?
2.9 years ago by n,n ▴ 360
1
vote
0
replies
606
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Does the GAF gene ontologies file only contain terms that are leaf nodes?
gene GO ontology
2.9 years ago by n,n ▴ 360
0
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1
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1.5k
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Comment: Comment: How to cite a pathway from wikipathways in text and in references in APA format
2.9 years ago by n,n ▴ 360
2
votes
2
replies
881
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Will quantile normalization affect the result of the Tau statistic?
RNA-Seq tissue-specificity tau
3.3 years ago by n,n ▴ 360
0
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0
replies
592
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Documentation on the contents of the "pubtatordb" package in R?
R pubtator
3.4 years ago by n,n ▴ 360
5
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8
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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
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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
0
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1
reply
1.3k
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Comment: C: Interpretation of "standardized expression matrix"?
3.9 years ago by n,n ▴ 360
0
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0
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1.3k
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Comment: C: Interpretation of "standardized expression matrix"?
3.9 years ago by n,n ▴ 360
0
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2
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1.3k
views
Comment: C: Interpretation of "standardized expression matrix"?
3.9 years ago by n,n ▴ 360
2
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6
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1.3k
views
Interpretation of "standardized expression matrix"?
RNA-Seq normalization
updated 3.9 years ago by 87k • written 3.9 years ago by ▴ 360
10
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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
0
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1
reply
2.0k
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Comment: C: Error using the getGEO() patcher
4.1 years ago by n,n ▴ 360
0
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1
reply
2.0k
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Comment: C: Error using the getGEO() patcher
4.1 years ago by n,n ▴ 360
0
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1
reply
2.0k
views
Comment: C: Error using the getGEO() patcher
4.1 years ago by n,n ▴ 360
3
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3
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2.8k
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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
3
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1
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1.3k
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Answer: A: Correlation vs differential expression testing
4.2 years ago by n,n ▴ 360
0
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0
replies
1.1k
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Extra adjustment variables during batch effect correction
rna-seq ComBat batch-effect
updated 8 days ago by 43k • written 4.3 years ago by ▴ 360
0
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1
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1.2k
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Comment: C: statistics method to find the relation between multiple variables of 50 samples
4.3 years ago by n,n ▴ 360
1
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1
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1.0k
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Comment: C: Can I use batch effect correction "by parts"?
4.3 years ago by n,n ▴ 360
0
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1
reply
1.0k
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Comment: C: Can I use batch effect correction "by parts"?
4.3 years ago by n,n ▴ 360
0
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1
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1.0k
views
Comment: C: Can I use batch effect correction "by parts"?
4.3 years ago by n,n ▴ 360
3
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7
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1.0k
views
Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 7 days ago by 43k • written 4.3 years ago by ▴ 360
0
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0
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785
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Comment: C: Time Series Network Identification (TSNI) data scaling
4.3 years ago by n,n ▴ 360
0
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2
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785
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Time Series Network Identification (TSNI) data scaling
expression TSNI
updated 4.3 years ago by ▴ 140 • written 4.3 years ago by ▴ 360
0
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1
reply
2.2k
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Comment: C: Should normalization of expression data be performed over the entire dataset or
4.4 years ago by n,n ▴ 360
4
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4
replies
2.2k
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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 4.4 years ago by ★ 7.0k • written 4.4 years ago by ▴ 360
0
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0
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4.0k
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Comment: C: Transcript vs. Gene TPM counts?
4.4 years ago by n,n ▴ 360
11
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7
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4.0k
views
Transcript vs. Gene TPM counts?
RNA-Seq GTEx GTEX
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by ▴ 360
0
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2
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4.0k
views
Comment: C: Transcript vs. Gene TPM counts?
4.5 years ago by n,n ▴ 360
0
votes
0
replies
736
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
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1
reply
1.0k
views
Download tissue distribution data from COSMIC?
database cosmic
updated 4.9 years ago by 20 • written 5.1 years ago by ▴ 360
0
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0
replies
914
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Comment: C: basic command in bash
5.5 years ago by n,n ▴ 360
0
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0
replies
2.4k
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Answer: A: blastp download option with csv
5.5 years ago by n,n ▴ 360
0
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1
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1.9k
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Comment: C: Extract sequences from the raw reads
5.5 years ago by n,n ▴ 360
3
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0
replies
1.5k
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Answer: A: counting number of genes located on positive or negative strands
5.5 years ago by n,n ▴ 360
1
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1
reply
1.1k
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Answer: A: need code for sorting fasta header
5.5 years ago by n,n ▴ 360
2
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1
reply
2.0k
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Answer: A: How to separate mixed orientation raw illumina sequence into forward and reverse
5.5 years ago by n,n ▴ 360
0
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0
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1.7k
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Comment: C: Faster way to get sequences from large fasta files?
5.5 years ago by n,n ▴ 360
1
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1
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1.7k
views
Answer: A: Faster way to get sequences from large fasta files?
5.5 years ago by n,n ▴ 360
0
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0
replies
1.0k
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Comment: C: gene expression for cancer identification
5.5 years ago by n,n ▴ 360
3
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0
replies
2.1k
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Answer: A: manipulating a file by R or bash?
5.5 years ago by n,n ▴ 360
1
vote
2
replies
5.2k
views
Answer: A: Join/Combine gff3 or gtf files
5.5 years ago by n,n ▴ 360
1
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1
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1.5k
views
Answer: A: How to write a proper bed file to extract sequence?
5.5 years ago by n,n ▴ 360
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