LMGene User’s Guide

Using the DSPCAD Integrative Command-Line Environment: User’s Guide for DICE

This document provides a user’s guide for DICE Version 1.0. The emphasis in this user’s guide is on providing detailed specifications for setting up and using the various features in DICE. For a general overview of DICE and descriptions of some of its core features, see Reference [1]. This user’s guide is supplemented by various materials that are available electronically from the DICE User’s G...

User’s Guide for YALL1: Your ALgorithms for L1 Optimization

This User’s Guide describes the functionality and basic usage of the Matlab package YALL1 for L1 minimization. The one-for-six algorithm used in the YALL1 solver is briefly introduced in the appendix.

User’s Guide for TVAL3: TV Minimization by Augmented Lagrangian and Alternating Direction Algorithms

This User’s Guide describes the functionality and basic usage of the Matlab package TVAL3 for total variation minimization. The main algorithm used in TVAL3 is briefly introduced in the appendix.

Analyzing WGBS with the bsseq package

This document discusses the ins and outs of an analysis of a whole-genome shotgun bisulfite sequencing (WGBS) dataset, using the BSmooth algorithm, which was first used in [1] and more formally presented and evaluated in [2]. The intention with the document is to focus on analysis-related tasks and questions. Basic usage of the bsseq package is covered in “The bsseq user’s guide”. It may be use...

GSS User’s Guide