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 3 months ago

13.05 score 77 stars 28 packages 2.3k scripts 4.8k 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 3 months ago

9.61 score 34 stars 5 packages 1.1k scripts 615 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 6 months ago

8.80 score 181 stars 1 packages 640 scripts 2.2k 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.

Last updated 9 months ago

arxivarxiv-analyticsarxiv-apiarxiv-org

7.25 score 60 stars 74 scripts 880 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 2 years ago

6.61 score 84 stars 322 scripts 457 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>.

Last updated 2 years ago

5.93 score 4 stars 1 packages 142 scripts 515 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).

Last updated 8 months ago

5.21 score 5 stars 1 packages 216 scripts 288 downloads

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>.

Last updated 4 months ago

5.17 score 4 stars 74 scripts 318 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.

Last updated 12 months ago

5.03 score 6 stars 18 scripts 172 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.

Last updated 4 months ago

4.68 score 2 stars 1 packages 16 scripts 258 downloads

chromer - Interface to Chromosome Counts Database API

A programmatic interface to the Chromosome Counts Database (<https://taux.evolseq.net/CCDB_web/>), Rice et al. (2014) <doi:10.1111/nph.13191>. This package is part of the 'ROpenSci' suite (<https://ropensci.org>).

Last updated 8 months ago

4.56 score 12 stars 4 scripts 279 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>.

Last updated 2 years ago

4.48 score 6 stars 5 scripts 167 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 2 years ago

3.85 score 14 scripts 189 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 2 years ago

3.76 score 4 stars 29 scripts 205 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>.

Last updated 2 years ago

3.63 score 5 stars 17 scripts 181 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>.

Last updated 1 years ago

3.35 score 3 stars 15 scripts 253 downloads

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>.

Last updated 2 years ago

2.70 score 1 stars 4 scripts 250 downloads