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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

13.30 score 89 stars 24 dependents 2.8k scripts 3.9k 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

10.20 score 40 stars 7 dependents 1.2k scripts 1.5k 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.

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9.83 score 183 stars 5 dependents 578 scripts 3.0k 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>.

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7.50 score 87 stars 344 scripts 554 downloads

aRxiv - 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.

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arxivarxiv-analyticsarxiv-apiarxiv-org

6.89 score 64 stars 603 downloads

miner - Control Minecraft with RaspberryJuice API

Following the code in py3minepi, allows one to connect to the minecraft from R.

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unconfunconf17

6.70 score 80 stars 1 dependents

lineup - 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. Broman et al. (2015) <doi:10.1534/g3.115.019778>.

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6.26 score 4 stars 102 scripts 377 downloads

qtl2convert - Convert Data among QTL Mapping Packages

Functions to convert data structures among the 'qtl2', 'qtl', and 'DOQTL' packages for mapping quantitative trait loci (QTL).

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cpp

6.23 score 5 stars 1 dependents 282 scripts 502 downloads

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.

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cpp

6.07 score 6 stars 28 scripts 373 downloads

regress - Gaussian Linear Models with Linear Covariance Structure

Functions to fit Gaussian linear model by maximising the residual log likelihood where the covariance structure can be written as a linear combination of known matrices. Can be used for multivariate models and random effects models. Easy straight forward manner to specify random effects models, including random interactions. Code now optimised to use Sherman Morrison Woodbury identities for matrix inversion in random effects models. We've added the ability to fit models using any kernel as well as a function to return the mean and covariance of random effects conditional on the data (best linear unbiased predictors, BLUPs). Clifford and McCullagh (2006) <https://www.r-project.org/doc/Rnews/Rnews_2006-2.pdf>.

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5.61 score 5 stars 163 scripts 542 downloads

qtl2fst - 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.

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5.56 score 2 stars 1 dependents 20 scripts 302 downloads

mbmixture - 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>.

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5.30 score 5 stars 6 scripts 302 downloads

craft - Extra Functions to Control Minecraft with RaspberryJuice API

Extra functions to illustrate the use of the miner package to control Minecraft with the RaspberryJuice API.

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4.82 score 11 stars

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

4.76 score 19 scripts 318 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>.

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4.68 score 4 stars 30 scripts 345 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

4.59 score 13 stars 348 downloads

mmconvert - 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>.

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cpp

4.06 score 4 stars 19 scripts 314 downloads

qtlbook - 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>.

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3.98 score 5 stars 19 scripts 307 downloads

lmmlite - Simple LMM Fitter for QTL Mapping

A port of parts of 'pylmm' for fitting linear mixed models relevant to genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping.

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cpp

3.86 score 12 stars 12 scripts

GNapi - Connection to the GeneNetwork API

Tools for connecting to the GeneNetwork API.

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3.85 score 6 scripts

detectPVC - Detect Premature Venticular Complexes

Detect premature ventricular complexes (PVCs) in data from a Polar H10 chest-strap heart rate sensor.

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3.78 score 2 stars 3 scripts

GWASapi - NHGRI-EBI GWAS Catalog of Summary Statistics

Tools for connecting to the NHGRI-EBI API for GWAS summary statistics.

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3.54 score 4 scripts

Rmaze - Generating Mazes with R

Generating mazes in R.

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3.48 score 1 dependents 6 scripts

negenes - 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>.

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3.30 score 1 stars 5 scripts 338 downloads

ricalc - Calculations for Recombinant Inbred Lines

Calculate two- and three-locus probabilities in multiple-strain recombinant inbred lines, and simulate such lines. Broman (2005) <doi:10.1534/genetics.104.035212>.

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2.65 score 3 stars 5 scripts

xoiGBS - Analyze Recombination and Crossover Interference with Sequence-Based Genotypes

Analyze recombination and crossover interference from genotyping-by-sequencing (GBS) data on a backcross.

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cpp

2.60 score 1 stars

npem - Analysis of Cell Proliferation Assays

Analysis of cell proliferation assays with a normal-Poisson mixture model. Broman et al. (1996) <doi:10.1016/S0022-1759(96)00136-6>.

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2.48 score 2 stars 6 scripts

geesibsor - Odds Ratio for Siblings by GEE

Estimate the odds ratio for siblings for a binary phenotype, adjusting for covariates, using generalized estimating equations.

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2.48 score 2 stars

fingers - Identifying Clusters of Related Individuals

Identifying clusters of related individuals.

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2.48 score 2 stars

qtl2cl - Command-Line Interface for R/qtl2

Support for a command-line interface for R/qtl2.

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2.48 score 2 stars 2 scripts