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BACKGROUND: the analysis of microbial communities through dna sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, vis...

We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions (i.e., coordinate traj...

Abstract This unit describes how to use BWA and the Genome Analysis Toolkit (GATK) to map genome sequencing data to a reference and produce high‐quality variant calls that can be used in downstream analyses. The comple...

BACKGROUND: Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis...

Subjects / keywords: Sampling (signal processing); Computer science; Identification (biology); Health informatics; Data science; Qualitative research; Selection (genetic algorithm); Management science; Data collection; Set (abstract data typ...

MOTIVATION: Prior biological knowledge greatly facilitates the meaningful interpretation of gene-expression data. Causal networks constructed from individual relationships curated from the literature are particularly sui...

BACKGROUND: System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new ...

SUMMARY: Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized ben...

Subjects / keywords: Computer science; Preprocessor; Human Connectome Project; Pipeline transport; Artifact (error); Data pre-processing; Connectome; Distortion (music); Artificial intelligence; Data mining; Computer vision; Pattern recognit...

Subjects / keywords: Data mining; Computer science; Electronic books

Covers supervised learning (prediction) to unsupervised learning. This book contains topics including neural networks, support vector machines, classification trees and boosting

Accelerating the discovery of advanced materials is essential for human welfare and sustainable, clean energy. In this paper, we introduce the Materials Project (www.materialsproject.org), a core program of the Materials...