Title: Preprocessing of Aligned Sequences from HTS Analyses
Author: Romain Fenouil, Nicolas Descostes, Lionel Spinelli, Jean-Christophe Andrau
Description: Pipeline and additional tools designed to handle aligned data from chromatin NGS experiments (less adapted for typical RNAseq applications). Specifically, starting from aligned reads after sequencing, the pipeline function aims at removing artefacts from datasets, estimate in-silico the fragments size, and generate WIG files with corrected values. The package also provides several tools for WIG files manipulations, scaling, merging and subtract (e.g. input).
Imports: bitops, tools, methods, S4Vectors, IRanges, GenomicRanges,
Depends: R (>= 3.2.0), parallel, GenomicAlignments
biocViews: ChIPSeq, Sequencing, Software, Preprocessing, Alignment

Author: Romain Fenouil, Nicolas Descostes, Lionel Spinelli, Frederic Koch, Muhammad Ahmad Maqbool, Touati Benoukraf, Pierre Cauchy, Charlene Innocenti, Pierre Ferrier, Jean-Christophe Andrau
ShortRead, Rsamtools, Biostrings, gtools, rtracklayer,

Title: Backwards Variable Selection for Paths using M Plus
Author: William Terry, Meredith Ray, Hongmei Zhang
Description: Primarily for use with datasets containing only categorical variables, although continuous variables may be included as independent variables in paths. Using M Plus, backward variable selection is performed on all Total, Total Indirect, and then Direct effects until none of these effects have p-values greater than the specified target p-value. If there are missing values in the data, imputations are performed using the Mice package. Then selection is performed with the imputed data sets, and results are averaged.

Title: Class-focused pattern metric comparisons using simulation
Author: Tarmo K. Remmel, (Marie-Josee Fortin, Ferenc Csillag, Sandor Kabos)
Maintainer: Tarmo K. Remmel <remmelt@yorku.ca>
Description: This library provides tools for estimating composition and configuration parameters from a categorical (binary) landscape map (grid) and then simulates a selected number of statistically similar landscapes.  Class-focused pattern metrics are computed for each simulated map to produce empirical distributions against which statistical comparisons can be made.  The code permits the analysis of single maps or pairs of maps.