Basic functions | Generating pedigrees | Example AIL pedigree matrix | Checking a pedigree matrix | RIL pedigree | 4-way cross pedigree | AIL pedigree | Diversity Outbred pedigree | Simulating from a pedigree | Generating marker data | Simulating multiple chromosomes | References

Example data | Lining up expression data | Lining up expression and genotype data | Conclusions

Introduction | Installation | Overview of craft commands | Building stuff | Useful tools | Drawing stuff | Games | Alternate setBlocks functions | Vector-based functions | Being Elsa from Frozen | Random walk | Dangerous functions | Acknowledgments and references

Introduction | Installation | About Minecraft | Your first miner adventure | Overview of miner commands | Suggestions for writing your own programs with miner | Details on Setting up a Minecraft server | Acknowledgments and References

Aligning rows or columns | Correlations between matrices | Correlations/distances between samples | Summarize correlations/distances | Identify sample mix-ups | Second-best samples | References

Installation | Basic use | Forming queries | Search terms | Subject classifications | Dates and ranges of dates | Search results | Sorting results | Technical details | Metadata limitations | Limit time between search requests | Limit number of items returned | Make requests in batches | License and bugs

Introduction | Installation | Usage

Examples | Example 1: Create an initial maze (maze with all walls on) | Example 2: Create mazes using different algorithms | Example 3: Step-by-step maze creation process | Example 4: Solving the maze | Example 5: Creating an imperfect maze

Fetch species list | Fetch Groups/RISets | Fetch genotypes for Group/RIset | Fetch datasets | Fetch sample data for dataset | Information for mRNA assay/probeset | Fetch individual phenotype info | Fetch trait information | Fetch sample data for a single trait | For mRNA expression/probeset | For classical phenotypes | Analyses | Gemma | R/qtl | Correlations

Installation | Lists of things | Get associations

Selecting one chromosome | Subsetting by ind, chr, mar | Binding by columns or rows | Looking under the hood | Paths | Direct construction of the fst database | Genome scans