A method that analyzes quality control metrics from multi-sample genomic sequencing studies and nominates poor quality samples for exclusion. Per sample quality control data are transformed into z-scores and aggregated. The distribution of aggregated z-scores are modelled using parametric distributions. The parameters of the optimal model, selected either by goodness-of-fit statistics or user-designation, are used for outlier nomination. Two implementations of the Cosine Similarity Outlier Detection algorithm are provided with flexible parameters for dataset customization.

Processing and analyzing omics data from genomics, transcriptomics, proteomics, and metabolomics platforms. It provides functions for preprocessing, normalization, visualization, and statistical analysis, as well as machine learning algorithms for predictive modeling. 'omicsTools' is an essential tool for researchers working with high-throughput omics data in fields such as biology, bioinformatics, and medicine.The QC-RLSC (quality control–based robust LOESS signal correction) algorithm is used for normalization. Dunn et al. (2011) <doi:10.1038/nprot.2011.335>.

In bulk epigenome/transcriptome experiments, molecular expression
    is measured in a tissue, which is a mixture of multiple types of cells.
    This package tests association of a disease/phenotype with a molecular marker
    for each cell type.
    The proportion of cell types in each sample needs to be given as input.
    The package is applicable to epigenome-wide association study (EWAS) and
    differential gene expression analysis.
    Takeuchi and Kato (submitted)
    "omicwas: cell-type-specific epigenome-wide and transcriptome association study".

Primarily devoted to implementing the Univariate Bootstrap (as well as the Traditional Bootstrap). In addition there are multiple functions for DeFries-Fulker behavioral genetics models. The univariate bootstrapping functions, DeFries-Fulker functions, regression and traditional bootstrapping functions form the original core. Additional features may come online later, however this software is a work in progress. For more information about univariate bootstrapping see: Lee and Rodgers (1998) and Beasley et al (2007) <doi:10.1037/1082-989X.12.4.414>.