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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]
To determine whether normalization is needed, one can plot Cy5 (R) intensities against Cy3 (G) intensities and see whether the slope of the line is around 1. An improved method, which is basically a scaled, 45 degree rotation of the R vs. G plot is an MA-plot. [ 4 ]
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.
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.
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. [1] [2]
The value computed with the CG function is unaffected by changes in the ordering of search results. That is, moving a highly relevant document above a higher ranked, less relevant, document does not change the computed value for CG (assuming ,). Based on the two assumptions made above about the usefulness of search results, (N)DCG is usually ...
^ = the maximized value of the likelihood function of the model , i.e. ^ = (^,), where {^} are the parameter values that maximize the likelihood function and is the observed data; n {\displaystyle n} = the number of data points in x {\displaystyle x} , the number of observations , or equivalently, the sample size;