Title: Differential Evolution-Based Bayesian Inference
Description: Bayesian inference algorithms based on the population-based "differential evolution" (DE) algorithm. Users can obtain posterior mode (MAP) estimates via DEMAP, posterior samples via DEMCMC, and variational approximations via DEVI.
Imports: stats, doParallel, randtoolbox, numDeriv
Author: Brendan Matthew Galdo [aut, cre]
Maintainer: Brendan Matthew Galdo <Brendan.m.galdo@gmail.com>

Title: DEComposition of Indirect and Direct Effects
Description: Calculates various estimates for measures of educational
differentials, the relative importance of primary and secondary
effects in the creation of such differentials and compares the

Packaged: 2014-11-27 12:56:37 UTC; ckartsonaki

Packaged: 2022-06-06 23:02:42 UTC; christianak

Title: Dirichlet-multinomial Evolutionary Event Profile Randomization
Author: Mark T Merilo <mmerilo@uoguelph.ca>
Maintainer: Mark T Merilo <mmerilo@uoguelph.ca>
Description: Tests for, and describe differences in event count profiles in groups of reconstructed cophylogenies

Title: Differential Expression Enrichment Tool
Description: A bio informatics R package for comparing a list of human genes to published RNA-Seq studies containing similar DE genes. Reference: Sokolowski,D.J., Ahn J., Erdman,L., Hou,H., Wang L., Goldenberg,A., and Wilson,M.D. (2022) Differential Expression Enrichment Tool (DEET): An interactive atlas of human differential gene expression. (In Preparation).
Imports: ActivePathways, pbapply, dplyr, ggplot2, glmnet, utils, stats,

Description: RNA sequencing (RNA-seq) followed by differential gene expression analyses is a fundamental approach for making biological discoveries. Ongoing large-scale efforts to systematically process and normalize publicly available gene expression data facilitate rapid reanalyses of specific studies and the development of new methods for querying it. While there are several powerful tools for querying systematically processed publicly available RNA-seq data at the individual sample level, there are fewer options for querying differentially expressed gene (DEG) lists generated from these experiments. Here, we present the Differential Expression Enrichment Tool (DEET), which allows users to interact with 3162 consistently processed DEG lists curated from 142 RNA-seq datasets obtained from recount2 database, which contains data from consortiums (GTex, TCGA) and individual labs (SRA). To establish DEET we integrated systematically processed human RNA-seq data from recount2 with reported and predicted metadata from multiple sources and developed a CRAN R package and Shiny App where users can compare their genes, p-values, and coefficients against the DEG lists within DEET. Here we present DEET and demonstrate how it can facilitate hypothesis generation and provide biological insight from user-defined differential gene expression results. Reference: Sokolowski,D.J., Ahn J., Erdman,L., Hou,H., Ellis,K., Wang L., Goldenberg,A., and Wilson,M.D. (2022) Differential Expression Enrichment Tool (DEET): An interactive atlas of human differential gene expression. (In Preparation).