Title: ANALYZING RNA SEQUENCE COUNT TABLES USING QUASI-LIKELIHOOD
person("Long", "Qu", role=c("aut", "cre","ctb"), email="long.qu@wright.edu"),
Description: Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative binomial models with 'QL', 'QLShrink' and 'QLSpline' methods (Lund, Nettleton, McCarthy, and Smyth, 2012).

Carlos A. de B. Pereira <cpereira@ime.usp.br>,
Maintainer: Cassio P. de Campos <cassiopc@acm.org>
Description: Functions to compute confidence statistics

Title: Processing Pipeline for 'SamBada' from Pre- To Post-Processing
Author: Solange Duruz, Sylvie Stucki, Oliver Selmoni, Elia Vajana
Description: Processing pipeline for 'SamBada' from pre- to post-processing.
'SamBada' is a landscape genomic software designed to run univariate or multivariate logistic regression between the presence of a genotype and one or several environmental variables. See Stucki (2017) <doi:10.1111/1755-0998.12629> and <https://github.com/Sylvie/sambada>.
The package provides functions that can be classified into four categories:
2) Preprocessing (prepare genomic file into standards compatible with 'SamBada' and apply quality-control; retrieve environmental conditions at sampling location; prepare environmental file including removal of correlated variables and computation of population structure)
3) Processing (run 'SamBada' on multiple cores using 'Supervision')
4) Post-processing (calculate p-values and q-values, produce interactive Manhattan plots and query 'Ensembl' database, produce maps).
Suggests: Rcpp, utils, data.table, shiny, plotly, httr, biomaRt,
ggplot2, sp, packcircles, raster, mapplots, spdep, rgdal,
gdalUtils, rworldmap, doParallel, foreach, knitr, rmarkdown

Title: Fast and light-weight caching of objects
Description: Methods for caching arbitrary R objects on persistent media.  Objects can be loaded and saved stratified on a set of hashing objects.
License: LGPL version 2.1 or newer (the releases)

Description: Methods for memoization, that is, caching arbitrary R objects in persistent memory.  Objects can be loaded and saved stratified on a set of hashing objects.