
qtl - Tools for Analyzing QTL Experiments
Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits. Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.
Last updated
openblas
13.32 score 88 stars 25 dependents 2.7k scripts 5.9k downloads
broman - Karl Broman's R Code
Miscellaneous R functions, including functions related to graphics (mostly for base graphics), permutation tests, running mean/median, and general utilities.
Last updated
10.04 score 183 stars 4 dependents 600 scripts 4.7k downloads
qtl2 - Quantitative Trait Locus Mapping in Experimental Crosses
Provides a set of tools to perform quantitative trait locus (QTL) analysis in experimental crosses. It is a reimplementation of the 'R/qtl' package to better handle high-dimensional data and complex cross designs. Broman et al. (2019) <doi:10.1534/genetics.118.301595>.
Last updated
cpp
9.82 score 39 stars 7 dependents 1.1k scripts 1.0k downloadsaRxiv - Interface to the arXiv API
An interface to the API for 'arXiv', a repository of electronic preprints for computer science, mathematics, physics, quantitative biology, quantitative finance, and statistics.
Last updated
arxivarxiv-analyticsarxiv-apiarxiv-org
7.93 score 64 stars 94 scripts 423 downloads
qtlcharts - Interactive Graphics for QTL Experiments
Web-based interactive charts (using D3.js) for the analysis of experimental crosses to identify genetic loci (quantitative trait loci, QTL) contributing to variation in quantitative traits. Broman (2015) <doi:10.1534/genetics.114.172742>.
Last updated
7.50 score 87 stars 345 scripts 733 downloads
miner - Control Minecraft with RaspberryJuice API
Following the code in py3minepi, allows one to connect to the minecraft from R.
Last updated
unconfunconf17
7.34 score 80 stars 1 dependents 52 scripts
simcross - Simulate Experimental Crosses
Simulate and plot general experimental crosses. The focus is on simulating genotypes with an aim towards flexibility rather than speed. Meiosis is simulated following the Stahl model, in which chiasma locations are the superposition of two processes: a proportion p coming from a process exhibiting no interference, and the remainder coming from a process following the chi-square model.
Last updated
cpp
6.03 score 6 stars 30 scripts 498 downloadsqtl2convert - Convert Data among QTL Mapping Packages
Functions to convert data structures among the 'qtl2', 'qtl', and 'DOQTL' packages for mapping quantitative trait loci (QTL).
Last updated
cpp
6.02 score 5 stars 1 dependents 282 scripts 564 downloadsmbmixture - Microbiome Mixture Analysis
Evaluate whether a microbiome sample is a mixture of two samples, by fitting a model for the number of read counts as a function of single nucleotide polymorphism (SNP) allele and the genotypes of two potential source samples. Lobo et al. (2021) <doi:10.1093/g3journal/jkab308>.
Last updated
5.18 score 5 stars 8 scripts 233 downloads
chromer - Interface to Chromosome Counts Database API
A programmatic interface to the Chromosome Counts Database (<https://ccdb.tau.ac.il/>), Rice et al. (2014) <doi:10.1111/nph.13191>. This package is part of the 'ROpenSci' suite (<https://ropensci.org>).
Last updated
4.89 score 13 stars 7 scripts 258 downloadsqtl2fst - Database Storage of Genotype Probabilities for QTL Mapping
Uses the 'fst' package to store genotype probabilities on disk for the 'qtl2' package. These genotype probabilities are a central data object for mapping quantitative trait loci (QTL), but they can be quite large. The facilities in this package enable the genotype probabilities to be stored on disk, leading to reduced memory usage with only a modest increase in computation time.
Last updated
4.78 score 2 stars 1 dependents 20 scripts 268 downloads
lineup2 - Lining Up Two Sets of Measurements
Tools for detecting and correcting sample mix-ups between two sets of measurements, such as between gene expression data on two tissues. This is a revised version of the 'lineup' package, to be more general and not tied to the 'qtl' package.
Last updated
cpp
4.70 score 20 scripts 256 downloads
xoi - Tools for Analyzing Crossover Interference
Analysis of crossover interference in experimental crosses, particularly regarding the gamma model. See, for example, Broman and Weber (2000) <doi:10.1086/302923>.
Last updated
4.56 score 4 stars 30 scripts 289 downloadsqtlbook - Datasets for the R/qtl Book
Datasets for the book, A Guide to QTL Mapping with R/qtl. Broman and Sen (2009) <doi:10.1007/978-0-387-92125-9>.
Last updated
3.98 score 5 stars 19 scripts 246 downloadsmmconvert - Mouse Map Converter
Convert mouse genome positions between the build 39 physical map and the genetic map of Cox et al. (2009) <doi:10.1534/genetics.109.105486>.
Last updated
cpp
3.86 score 4 stars 18 scripts 188 downloadsGNapi - Connection to the GeneNetwork API
Tools for connecting to the GeneNetwork API.
Last updated
3.70 score 5 scripts
detectPVC - Detect Premature Venticular Complexes
Detect premature ventricular complexes (PVCs) in data from a Polar H10 chest-strap heart rate sensor.
Last updated
3.60 score 2 stars 3 scriptsGWASapi - NHGRI-EBI GWAS Catalog of Summary Statistics
Tools for connecting to the NHGRI-EBI API for GWAS summary statistics.
Last updated
3.40 score 4 scriptsnegenes - Estimating the Number of Essential Genes in a Genome
Estimating the number of essential genes in a genome on the basis of data from a random transposon mutagenesis experiment, through the use of a Gibbs sampler. Lamichhane et al. (2003) <doi:10.1073/pnas.1231432100>.
Last updated
3.30 score 1 stars 5 scripts 259 downloadsfingers - Identifying Clusters of Related Individuals
Identifying clusters of related individuals.
Last updated
2.48 score 2 starsqtl2cl - Command-Line Interface for R/qtl2
Support for a command-line interface for R/qtl2.
Last updated
2.48 score 2 stars 2 scriptslabstat - Statistics for Lab Scientists
Data and code for a course in statistics for laboratory scientists.
Last updated
2.48 score 2 starsqtlsim - Software for Testing QTL Analysis via Simulations
Software for testing QTL analysis via simulations.
Last updated
2.18 score 1 stars


