These repositories study methods for Systems Genetics, Systems Genomics and Omics. I have been involved in this work for over 25 years. The vast majority concern gene mapping, or QTLs. They are organized by subject under dropdown menus.
QTL Repos
QTL stands for
quantitative trait loci,
which is also known as gene mapping.
Recent work builds on Karl Broman's
R/qtl2
package,
offering ggplot2 functionality as well as deeper dives into
SNP
patterns.
The qtl2shiny package provides a friendly interface to investigate local QTL behavior.
It draws on mediation repos found in another dropdown menu.
Earlier work builds on Broman's
R/qtl
package, and includes some useful features (notably hotspot analysis) not yet fully migrated to R/qtl2.
| repo | title | type |
|---|---|---|
qtl2 |
QTL analysis software for high-dimensional data and complex cross designs | Broman R/qtl2 |
qtl2fst |
R/qtl2 package using fst to store genotype probabilities | Broman R/qtl2fst |
qtl2ggplot |
Extension of R/qtl2plot to ggplot2 | R graphics |
qtl2pattern |
Pattern support for R/qtl2 | R analysis |
qtl2shiny |
Shiny app for R/qtl2 | R shiny |
qtl2hot |
Hot Spot Analysis with Qtl2 | R analysis in devel |
qtl |
Branch of Karl Broman's R/qtl | Broman R/qtl |
qtlbim |
QTL Bayesian Interval Mapping | R analysis |
qtlnet |
Infer QTL genetic architecture and causal network for set of correlated traits | R analysis |
qtlhot |
QTL hotspot inference | R analysis |
qtlbcsft |
Tools for testing QTL BCsFt calculations | R analysis |
qtlyeast |
QTL Analysis of Brem Kruglyak Yeast Data | R data |
Mediation Repos
Mediation repos build on the excellent work of
Elias Chaibub Neto
on causal model selection tests.
This is incorporated into the qtl2shiny app cited in the QTL dropdown menu.
| repo | title | type |
|---|---|---|
intermediate |
small R utility for mediation analysis | Churchill Lab |
qtl2mediate |
Mediation using package qtl2 | R analysis |
Tmem68 |
Tmem68 mRNA Data example from Chick et al. 2016 | Churchill Lab |
qtlcmst |
QTL Causal Model Selection Tests | R analysis |
CausalMST |
Causal Model Selection Hypothesis Tests | see intermediate and qtl2mediate |
qdg |
QTL Directed Graphs | R analysis defunct? |
Founder Repos
These repos study the
Collaborative Cross (CC)
mouse founder lines.
See foundr for information about deployed shiny apps.
| repo | title | type |
|---|---|---|
foundr |
Multiparent Founder Study Tools | R analysis |
foundrShiny |
Shiny app tools for foundr package | R shiny |
foundrHarmony |
Harmonize data for foundr analysis and visualization | R tidy data |
metabr |
Metabolite Data Processing | R analysis |
modulr |
Trait Module Creation and Analysis | R analysis |
Attie Lab Repos
These repos are specific to collaboration with the Alan Attie Lab at UW-Madison Biochemistry. This is part of a long-term collaboration (>25 years) that has inspired much of my work.
| repo | title | type |
|---|---|---|
FounderDietStudy |
Founder Diet Study Application | Attie Lab |
FounderCalciumStudy |
Founder Calcium Study Application | Attie Lab |
DO_Diet |
DO Diet Study Application | Attie Lab |
AttieDOv2 |
Attie DO 500 Study Application | R tidy data |
Other Repos
These other repos include a workshop in Thailand in 2017 and various projects that have not moved forward.
| repo | title | type |
|---|---|---|
PlantSysGen |
Thailand Plant Systems Genetics Workshop 2017 | R analysis |
thailand |
Thailand Plant Systems Genetics Workshop 2017 | HTML presentation |
qtl2rmd |
Rmarkdown for qtl2 analyses | R analysis defunct? |
qtl2feather |
R/qtl2 package using feather to store genotype probabilities | R analysis defunct? |
CCSanger |
Pull Sanger features for CC founder strains | R analysis defunct? |
qtl2biome |
R/qtl2 package for microbiome data analysis | R early stages |
Rbiodalliance |
R wrapper for biodalliance.org | R analysis defunct? |
qtlview](https://github.com/byandell-sysgen/qtlview) |
Utilities to view QTL results on the Web | R graphics defunct? |