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In addition to size factor normalization, DESeq2 also employs a variance-stabilizing transformation, which further enhances the quality of the data by stabilizing the variance across different expression levels. [4] This combination of normalization techniques minimizes bias and improves the accuracy of differential expression analysis.
Using DESeq2 as a framework, DEvis provides a wide variety of tools for data manipulation, visualization, and project management. DEXSeq is Bioconductor package that finds differential differential exon usage based on RNA-Seq exon counts between samples. DEXSeq employs negative binomial distribution, provides options to visualization and ...
Methods: Most tools use regression or non-parametric statistics to identify differentially expressed genes, and are either based on read counts mapped to a reference genome (DESeq2, limma, edgeR) or based on read counts derived from alignment-free quantification (sleuth, [106] Cuffdiff, [107] Ballgown [108]). [109]
Within computational biology, an MA plot is an application of a Bland–Altman plot for visual representation of genomic data. The plot visualizes the differences between measurements taken in two samples, by transforming the data onto M (log ratio) and A (mean average) scales, then plotting these values.
In another usage in statistics, normalization refers to the creation of shifted and scaled versions of statistics, where the intention is that these normalized values allow the comparison of corresponding normalized values for different datasets in a way that eliminates the effects of certain gross influences, as in an anomaly time series. Some ...
In computing, a keyboard shortcut is a sequence or combination of keystrokes on a computer keyboard which invokes commands in software. Most keyboard shortcuts require the user to press a single key or a sequence of keys one after the other. Other keyboard shortcuts require pressing and holding several keys simultaneously (indicated in the ...
To quantile normalize two or more distributions to each other, without a reference distribution, sort as before, then set to the average (usually, arithmetic mean) of the distributions. So the highest value in all cases becomes the mean of the highest values, the second highest value becomes the mean of the second highest values, and so on.
The softmax function, also known as softargmax [1]: 184 or normalized exponential function, [2]: 198 converts a vector of K real numbers into a probability distribution of K possible outcomes. It is a generalization of the logistic function to multiple dimensions, and is used in multinomial logistic regression .