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r-mbcluster.seq
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public |
Cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data
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2025-04-22 |
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r-mbc
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Calibrate and apply multivariate bias correction algorithms for climate model simulations of multiple climate variables. Three methods described by Cannon (2016) <doi:10.1175/JCLI-D-15-0679.1> and Cannon (2018) <doi:10.1007/s00382-017-3580-6> are implemented: (i) MBC Pearson correlation (MBCp), (ii) MBC rank correlation (MBCr), and (iii) MBC N-dimensional PDF transform (MBCn).
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2025-04-22 |
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r-mazeinda
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Methods for calculating and testing the significance of pairwise monotonic association from and based on the work of Pimentel (2009) <doi:10.4135/9781412985291.n2>. Computation of association of vectors from one or multiple sets can be performed in parallel thanks to the packages 'foreach' and 'doMC'.
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2025-04-22 |
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r-mazegen
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A maze generator that creates the Elithorn Maze (HTML file) and the functions to calculate the associated maze parameters (i.e. Difficulty and Ability).
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2025-04-22 |
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r-maxskew
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It finds Orthogonal Data Projections with Maximal Skewness. The first data projection in the output is the most skewed among all linear data projections. The second data projection in the output is the most skewed among all data projections orthogonal to the first one, and so on.
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2025-04-22 |
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r-maxnet
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public |
Procedures to fit species distributions models from occurrence records and environmental variables, using 'glmnet' for model fitting. Model structure is the same as for the 'Maxent' Java package, version 3.4.0, with the same feature types and regularization options. See the 'Maxent' website <http://biodiversityinformatics.amnh.org/open_source/maxent> for more details.
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2025-04-22 |
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r-maxmatching
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Computes the maximum matching for unweighted graph and maximum matching for (un)weighted bipartite graph efficiently.
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2025-04-22 |
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r-maxlike
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Provides a likelihood-based approach to modeling species distributions using presence-only data. In contrast to the popular software program MAXENT, this approach yields estimates of the probability of occurrence, which is a natural descriptor of a species' distribution.
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2025-04-22 |
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r-mavtgsa
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This package is a gene set analysis function for one-sided test (OLS), two-sided test (multivariate analysis of variance). If the experimental conditions are equal to 2, the p-value for Hotelling's t^2 test is calculated. If the experimental conditions are great than 2, the p-value for Wilks' Lambda is determined and post-hoc test is reported too. Three multiple comparison procedures, Dunnett, Tukey, and sequential pairwise comparison, are implemented. The program computes the p-values and FDR (false discovery rate) q-values for all gene sets. The p-values for individual genes in a significant gene set are also listed. MAVTgsa generates two visualization output: a p-value plot of gene sets (GSA plot) and a GST-plot of the empirical distribution function of the ranked test statistics of a given gene set. A Random Forests-based procedure is to identify gene sets that can accurately predict samples from different experimental conditions or are associated with the continuous phenotypes.
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2025-04-22 |
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r-mattools
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This package in includes functions for receiver operating characteristic (ROC) analyses as well as Monte Carlo simulation. It includes specific graphical functions for interpreting the output of these techniques.
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2025-04-22 |
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r-matskew
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Performs matrix skew-t parameter estimation, Gallaugher and McNicholas (2017) <doi: 10.1002/sta4.143>.
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2025-04-22 |
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r-matrixtests
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Functions to perform fast statistical hypothesis tests on rows/columns of matrices. The main goals are: 1) speed via vectorization, 2) output that is detailed and easy to use, 3) compatibility with tests implemented in R (like those available in the 'stats' package).
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2025-04-22 |
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r-matrixstructest
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Tests for block-diagonal structure in symmetric matrices (e.g. correlation matrices) under the null hypothesis of exchangeable off-diagonal elements. As described in Segal et al. (2019), these tests can be useful for construct validation either by themselves or as a complement to confirmatory factor analysis. Monte Carlo methods are used to approximate the permutation p-value with Hubert's Gamma (Hubert, 1976) and a t-statistic. This package also implements the chi-squared statistic described by Steiger (1980). Please see Segal, et al. (2019) <doi:10.1007/s11336-018-9647-4> for more information.
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2025-04-22 |
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r-matrixnormal
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Computes densities, probabilities, and random deviates of the Matrix Normal (Iranmanesh et al. (2010) <doi:10.7508/ijmsi.2010.02.004>). Also includes simple but useful matrix functions. See the vignette for more information.
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2025-04-22 |
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r-matrixeqtl
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Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix eQTL can test for association between genotype and gene expression using linear regression with either additive or ANOVA genotype effects. The models can include covariates to account for factors as population stratification, gender, and clinical variables. It also supports models with heteroscedastic and/or correlated errors, false discovery rate estimation and separate treatment of local (cis) and distant (trans) eQTLs.
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2025-04-22 |
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r-matrixcalc
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A collection of functions to support matrix calculations for probability, econometric and numerical analysis. There are additional functions that are comparable to APL functions which are useful for actuarial models such as pension mathematics. This package is used for teaching and research purposes at the Department of Finance and Risk Engineering, New York University, Polytechnic Institute, Brooklyn, NY 11201.
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2025-04-22 |
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r-matpow
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A general framework for computing powers of matrices. A key feature is the capability for users to write callback functions, called after each iteration, thus enabling customization for specific applications. Diverse types of matrix classes/matrix multiplication are accommodated. If the multiplication type computes in parallel, then the package computation is also parallel.
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2025-04-22 |
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r-matlabr
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Provides users to call MATLAB from using the "system" command. Allows users to submit lines of code or MATLAB m files. This is in comparison to 'R.matlab', which creates a MATLAB server.
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2025-04-22 |
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r-matlab
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Emulate MATLAB code using R
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2025-04-22 |
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r-mathgraph
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Simple tools for constructing and manipulating objects of class mathgraph from the book "S Poetry", available at <http://www.burns-stat.com/pages/spoetry.html>.
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2025-04-22 |
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r-matconv
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Transferring over a code base from Matlab to R is often a repetitive and inefficient use of time. This package provides a translator for Matlab / Octave code into R code. It does some syntax changes, but most of the heavy lifting is in the function changes since the languages are so similar. Options for different data structures and the functions that can be changed are given. The Matlab code should be mostly in adherence to the standard style guide but some effort has been made to accommodate different number of spaces and other small syntax issues. This will not make the code more R friendly and may not even run afterwards. However, the rudimentary syntax, base function and data structure conversion is done quickly so that the maintainer can focus on changes to the design structure.
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2025-04-22 |
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r-matchbook
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Provides a wrapper for the some basic functionality around the 'Matchbook' <http://www.matchbook.com> REST API. It features calls to get events, markets and runners in data frame format. It features functions for bet placement and position management and also allows reporting of settled bet transactions. Note: this package uses the back-lay format. The default for odds type, currency and language are set according to those of the registered user account.
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2025-04-22 |
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r-mata
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Calculates Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals, which are constructed using single-model estimators and model weights. See Turek and Fletcher (2012) <doi:10.1016/j.csda.2012.03.002> for details.
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2025-04-22 |
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r-masstimate
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Estimation equations are from a variety of sources but are, in general, based on regressions between skeletal measurements (e.g., femoral circumference) and body mass in living taxa.
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2025-04-22 |
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r-massign
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Constructing matrices for quick prototyping can be a nuisance, requiring the user to think about how to fill the matrix with values using the matrix() function. The %<-% operator solves that issue by allowing the user to construct matrices using code that shows the actual matrices.
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2025-04-22 |
