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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 ...
DESeq2 employs statistical methods to normalize and analyze RNA-seq data, making it a valuable tool for researchers studying gene expression patterns and regulation. It is available through the Bioconductor repository. It was first presented in 2014. [1] As of September 2023, its use has been cited over 30,000 times. [2]
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.
Normal probability plots are made of raw data, residuals from model fits, and estimated parameters. A normal probability plot. In a normal probability plot (also called a "normal plot"), the sorted data are plotted vs. values selected to make the resulting image look close to a straight line if the data are approximately normally distributed.
In digital signal processing (DSP), a normalized frequency is a ratio of a variable frequency and a constant frequency associated with a system (such as a sampling rate, ). Some software applications require normalized inputs and produce normalized outputs, which can be re-scaled to physical units when necessary.
Volcano plots show a characteristic upwards two arm shape because the x axis, i.e. the underlying log 2-fold changes, are generally normal distribution whereas the y axis, the log 10-p values, tend toward greater significance for fold-changes that deviate more strongly from zero. The density of the normal distribution takes the form
Label-free quantification is a method in mass spectrometry that aims to determine the relative amount of proteins in two or more biological samples. Unlike other methods for protein quantification, label-free quantification does not use a stable isotope containing compound to chemically bind to and thus label the protein.
In probability theory and statistics, the index of dispersion, [1] dispersion index, coefficient of dispersion, relative variance, or variance-to-mean ratio (VMR), like the coefficient of variation, is a normalized measure of the dispersion of a probability distribution: it is a measure used to quantify whether a set of observed occurrences are clustered or dispersed compared to a standard ...