Description: A computational method developed for model-based analysis of alternative polyadenylation (APA) using 3' end-linked reads. It accurately assigns 3' RNA-seq reads to polyA sites through statistical modeling, and generates multiple statistics for APA analysis. Please also see Li WV, Zheng D, Wang R, Tian B (2021) <doi:10.1186/s13059-021-02429-5>.

Title: Multi-Armed Bayesian Ordinal Utility-Based Sequential Trial
Description: Conducts and simulates the MABOUST design, including making interim decisions to stop a treatment for inferiority or stop the trial early for superiority or equivalency.

Title: Molecular Acquisition, Cleaning, and Evaluation in R 'MACER'
Maintainer: Robert G Young <rgyoung6@gmail.com>
Description: To assist biological researchers in assembling taxonomically and marker focused molecular sequence data sets. 'MACER' accepts a list of genera as a user input and uses NCBI-GenBank and BOLD as resources to download and assemble molecular sequence datasets. These datasets are then assembled by marker, aligned, trimmed, and cleaned. The use of this package allows the publication of specific parameters to ensure reproducibility. The 'MACER' package has four core functions and an example run through using all of these functions can be found in the associated repository <https://github.com/rgyoung6/MACER_example>.
Imports: rentrez (>= 1.2.2), ape (>= 5.5), httr, stats, utils

Imports: rentrez, ape, httr, stats, utils

Imports: rentrez, ape, httr, stats, utils, ggplot2, parallel, pbapply,

Title: This package provides some basic methods for meta-analysis
Description: In this package we provide some basic utilities for
performing meta-analysis. We included methods for dealing with
missing values, or measurements with a variance of zero. For
developing or testing meta-analysis methods a mock up data
model is integrated. Additionally did we implement a method for
performing significance based methods proposed by Fisher and
Rhodes. For visualizing the results three methods were added.
Depends: R (>= 2.9), Biobase (>= 2.4), snow, qvalue, RankProd
Imports: RColorBrewer, GeneMeta, gplots, genefilter, impute