In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
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/pdf/moderated-estimation-of-fold-change-and-dispersion-for-rna-3ywnbkcan0.pdf

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-Seq data, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data. DESeq2 uses shrinkage estimation for dispersions and fold changes to improve stability and interpretability of the estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression and facilitates downstream tasks such as gene ranking and visualization. DESeq2 is available as an R/Bioconductor package.

/pdf/moderated-estimation-of-fold-change-and-dispersion-for-rna-59glcgpwlk.pdf

Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.

/pdf/arlequin-version-3-0-an-integrated-software-package-for-4cs6nd3y2p.pdf

Arlequin (version 3.0): An integrated software package for population genetics data analysis

: This reprint will introduce and study the most basic properties of three new variational problems which are suggested by applications to computer vision. In computer vision, a fundamental problem is to appropriately decompose the domain R of a function g (x,y) of two variables. This problem starts by describing the physical situation which produces images: assume that a three-dimensional world is observed by an eye or camera from some point P and that g1(rho) represents the intensity of the light in this world approaching the point sub 1 from a direction rho. If one has a lens at P focusing this light on a retina or a film-in both cases a plane domain R in which we may introduce coordinates x, y then let g(x,y) be the strength of the light signal striking R at a point with coordinates (x,y); g(x,y) is essentially the same as sub 1 (rho) -possibly after a simple transformation given by the geometry of the imaging syste. The function g(x,y) defined on the plane domain R will be called an image. What sort of function is g? The light reflected off the surfaces Si of various solid objects O sub i visible from P will strike the domain R in various open subsets R sub i. When one object O1 is partially in front of another object O2 as seen from P, but some of object O2 appears as the background to the sides of O1, then the open sets R1 and R2 will have a common boundary (the 'edge' of object O1 in the image defined on R) and one usually expects the image g(x,y) to be discontinuous along this boundary. (JHD)

/pdf/optimal-approximations-by-piecewise-smooth-functions-and-2t87isujr0.pdf

Optimal approximations by piecewise smooth functions and associated variational problems

The statistical properties of least-squares frequency analysis of unequally spaced data are examined. It is shown that, in the least-squares spectrum of gaussian noise, the reduction in the sum of squares at a particular frequency is aX22 variable. The reductions at different frequencies are not independent, as there is a correlation between the height of the spectrum at any two frequencies,f1 andf2, which is equal to the mean height of the spectrum due to a sinusoidal signal of frequencyf1, at the frequencyf2. These correlations reduce the distortion in the spectrum of a signal affected by noise. Some numerical illustrations of the properties of least-squares frequency spectra are also given.

Donald A. McQuarrie

Papers

Handbook of Mathematical Functions

Multiplet Structure of Atoms and Molecules

Differential Equations of Applied Mathematics