The following repositories are roughly organized by project.
| repo | title | other |
|---|---|---|
qtl2 |
QTL analysis software for high-dimensional data and complex cross designs | Broman R/qtl2 |
qtl |
Branch of Karl Broman's R/qtl | Broman R/qtl |
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 |
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 |
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? |
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 |
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 |
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 |
Utilities to view QTL results on the Web | R graphics defunct? |