|
r-mangotraining
|
public |
Datasets designed to be used in conjunction with Mango Solutions training materials and the book SAMS Teach Yourself R in 24 Hours (ISBN: 978-0-672-33848-9).
|
2023-06-16 |
|
r-malani
|
public |
Find dark genes. These genes are often disregarded due to no detected mutation or differential expression, but are important in coordinating the functionality in cancer networks.
|
2023-06-16 |
|
r-lsd
|
public |
Create lots of colorful plots in a plethora of variations. Try the LSD demotour().
|
2023-06-16 |
|
r-logicoil
|
public |
This package contains the functions necessary to run the LOGICOIL algorithm. LOGICOIL can be used to differentiate between antiparallel dimers, parallel dimers, trimers and higher-order coiled-coil sequence. By covering >90 percent of the known coiled-coil structures, LOGICOIL is a net improvement compared with other existing methods, which achieve a predictive coverage of around 31 percent of this population. As such, LOGICOIL is particularly useful for researchers looking to characterize novel coiled-coil sequences or studying coiled-coil containing protein assemblies. It may also be used to assist in the structural characterization of synthetic coiled-coil sequences.
|
2023-06-16 |
|
r-listenv
|
public |
List environments are environments that have list-like properties. For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting, e.g. 'x <- listenv(a = 1, b = 2); for (i in seq_along(x)) x[[i]] <- x[[i]] ^ 2; y <- as.list(x)'.
|
2023-06-16 |
|
r-lisa
|
public |
Contains 128 palettes from Color Lisa. All palettes are based on masterpieces from the worlds greatest artists. For more information, see <http://colorlisa.com/>.
|
2023-06-16 |
|
r-linselect
|
public |
Estimate the mean of a Gaussian vector, by choosing among a large collection of estimators. In particular it solves the problem of variable selection by choosing the best predictor among predictors emanating from different methods as lasso, elastic-net, adaptive lasso, pls, randomForest. Moreover, it can be applied for choosing the tuning parameter in a Gauss-lasso procedure.
|
2023-06-16 |
|
r-linl
|
public |
A 'LaTeX' Letter class for 'rmarkdown', using the 'pandoc-letter' template adapted for use with 'markdown'.
|
2023-06-16 |
|
r-lgrdata
|
public |
A largish collection of example datasets, including several classics. Many of these datasets are well suited for regression, classification, and visualization.
|
2023-06-16 |
|
r-lgr
|
public |
A flexible, feature-rich yet light-weight logging framework based on 'R6' classes. It supports hierarchical loggers, custom log levels, arbitrary data fields in log events, logging to plaintext, 'JSON', (rotating) files, memory buffers, and databases, as well as email and push notifications. For a full list of features with examples please refer to the package vignette.
|
2023-06-16 |
|
r-lenses
|
public |
Provides tools for creating and using lenses to simplify data manipulation. Lenses are composable getter/setter pairs for working with data in a purely functional way. Inspired by the 'Haskell' library 'lens' (Kmett, 2012) <https://hackage.haskell.org/package/lens>. For a fairly comprehensive (and highly technical) history of lenses please see the 'lens' wiki <https://github.com/ekmett/lens/wiki/History-of-Lenses>.
|
2023-06-16 |
|
r-leap
|
public |
Advances in sequencing technology now allow researchers to capture the expression profiles of individual cells. Several algorithms have been developed to attempt to account for these effects by determining a cell's so-called `pseudotime', or relative biological state of transition. By applying these algorithms to single-cell sequencing data, we can sort cells into their pseudotemporal ordering based on gene expression. LEAP (Lag-based Expression Association for Pseudotime-series) then applies a time-series inspired lag-based correlation analysis to reveal linearly dependent genetic associations.
|
2023-06-16 |
|
r-nmi
|
public |
Calculates the normalized mutual information (NMI) of two community structures in network analysis.
|
2023-06-16 |
|
r-nlwaldtest
|
public |
Wald Test for nonlinear restrictions on model parameters and confidence intervals for nonlinear functions of parameters using delta-method. Applicable after ANY model, provided parameters estimates and their covariance matrix are available.
|
2023-06-16 |
|
r-neat
|
public |
Includes functions and examples to compute NEAT, the Network Enrichment Analysis Test described in Signorelli et al. (2016, <DOI:10.1186/s12859-016-1203-6>).
|
2023-06-16 |
|
r-nbclust
|
public |
It provides 30 indexes for determining the optimal number of clusters in a data set and offers the best clustering scheme from different results to the user.
|
2023-06-16 |
|
r-mycobacrvr
|
public |
The mycobacrvR package contains utilities to provide detailed information for B cell and T cell epitopes for predicted adhesins from various servers such as ABCpred, Bcepred, Bimas, Propred, NetMHC and IEDB. Please refer the URL below to download data files (data_mycobacrvR.zip) used in functions of this package.
|
2023-06-16 |
|
r-mwshiny
|
public |
A simple function, mwsApp(), that runs a 'shiny' app spanning multiple, connected windows. This uses all standard 'shiny' conventions, and depends only on the 'shiny' package.
|
2023-06-16 |
|
r-mvshapirotest
|
public |
This package implements the generalization of the Shapiro-Wilk test for multivariate normality proposed by Villasenor-Alva and Gonzalez-Estrada (2009).
|
2023-06-16 |
|
r-mvglmmrank
|
public |
Maximum likelihood estimates are obtained via an EM algorithm with either a first-order or a fully exponential Laplace approximation.
|
2023-06-16 |
|
r-multiwave
|
public |
Computation of an estimation of the long-memory parameters and the long-run covariance matrix using a multivariate model (Lobato (1999) <doi:10.1016/S0304-4076(98)00038-4>; Shimotsu (2007) <doi:10.1016/j.jeconom.2006.01.003>). Two semi-parametric methods are implemented: a Fourier based approach (Shimotsu (2007) <doi:10.1016/j.jeconom.2006.01.003>) and a wavelet based approach (Achard and Gannaz (2016) <doi:10.1111/jtsa.12170>).
|
2023-06-16 |
|
r-multisom
|
public |
Implements two versions of the algorithm namely: stochastic and batch. The package determines also the best number of clusters and offers to the user the best clustering scheme from different results.
|
2023-06-16 |
|
r-muckrock
|
public |
A data package containing public domain information on requests made by the 'MuckRock' (https://www.muckrock.com/) project under the United States Freedom of Information Act.
|
2023-06-16 |
|
r-msbox
|
public |
Common mass spectrometry tools described in John Roboz (2013) <doi:10.1201/b15436>. It allows checking element isotopes, calculating (isotope labelled) exact monoisitopic mass, m/z values and mass accuracy, and inspecting possible contaminant mass peaks, examining possible adducts in electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) ion sources.
|
2023-06-16 |
|
r-motilitylab
|
public |
Statistics to quantify tracks of moving things (x-y-z-t data), such as cells, bacteria or animals. Available measures include mean square displacement, confinement ratio, autocorrelation, straightness, turning angle, and fractal dimension.
|
2023-06-16 |
|
r-modehunt
|
public |
Given independent and identically distributed observations X(1), ..., X(n) from a density f, provides five methods to perform a multiscale analysis about f as well as the necessary critical values. The first method, introduced in Duembgen and Walther (2008), provides simultaneous confidence statements for the existence and location of local increases (or decreases) of f, based on all intervals I(all) spanned by any two observations X(j), X(k). The second method approximates the latter approach by using only a subset of I(all) and is therefore computationally much more efficient, but asymptotically equivalent. Omitting the additive correction term Gamma in either method offers another two approaches which are more powerful on small scales and less powerful on large scales, however, not asymptotically minimax optimal anymore. Finally, the block procedure is a compromise between adding Gamma or not, having intermediate power properties. The latter is again asymptotically equivalent to the first and was introduced in Rufibach and Walther (2010).
|
2023-06-16 |
|
r-modalclust
|
public |
Performs Modal Clustering (MAC) including Hierarchical Modal Clustering (HMAC) along with their parallel implementation (PHMAC) over several processors. These model-based non-parametric clustering techniques can extract clusters in very high dimensions with arbitrary density shapes. By default clustering is performed over several resolutions and the results are summarised as a hierarchical tree. Associated plot functions are also provided. There is a package vignette that provides many examples. This version adheres to CRAN policy of not spanning more than two child processes by default.
|
2023-06-16 |
|
r-mod09nrt
|
public |
Package for processing downloaded MODIS Surface reflectance Product HDF files. Specifically, MOD09 surface reflectance product files, and the associated MOD03 geolocation files (for MODIS-TERRA). The package will be most effective if the user installs MRTSwath (MODIS Reprojection Tool for swath products; <https://lpdaac.usgs.gov/tools/modis_reprojection_tool_swath>, and adds the directory with the MRTSwath executable to the default R PATH by editing ~/.Rprofile.
|
2023-06-16 |
|
r-mmtsne
|
public |
An implementation of multiple maps t-distributed stochastic neighbor embedding (t-SNE). Multiple maps t-SNE is a method for projecting high-dimensional data into several low-dimensional maps such that non-metric space properties are better preserved than they would be by a single map. Multiple maps t-SNE with only one map is equivalent to standard t-SNE. When projecting onto more than one map, multiple maps t-SNE estimates a set of latent weights that allow each point to contribute to one or more maps depending on similarity relationships in the original data. This implementation is a port of the original 'Matlab' library by Laurens van der Maaten. See Van der Maaten and Hinton (2012) <doi:10.1007/s10994-011-5273-4>. This material is based upon work supported by the United States Air Force and Defense Advanced Research Project Agency (DARPA) under Contract No. FA8750-17-C-0020. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the United States Air Force and Defense Advanced Research Projects Agency. Distribution Statement A: Approved for Public Release; Distribution Unlimited.
|
2023-06-16 |
|
r-mlsjunkgen
|
public |
Generate a stream of pseudo-random numbers generated using the MLS Junk Generator algorithm. Functions exist to generate single pseudo-random numbers as well as a vector, data frame, or matrix of pseudo-random numbers.
|
2023-06-16 |
|
r-mixrasch
|
public |
Estimates Rasch models and mixture Rasch models, including the dichotomous Rasch model, the rating scale model, and the partial credit model.
|
2023-06-16 |
|
r-mixemm
|
public |
Contains functions for estimating a mixed-effects model for clustered data (or batch-processed data) with cluster-level (or batch- level) missing values in the outcome, i.e., the outcomes of some clusters are either all observed or missing altogether. The model is developed for analyzing incomplete data from labeling-based quantitative proteomics experiments but is not limited to this type of data. We used an expectation conditional maximization (ECM) algorithm for model estimation. The cluster-level missingness may depend on the average value of the outcome in the cluster (missing not at random).
|
2023-06-16 |
|
r-mft
|
public |
Provides statistical tests and algorithms for the detection of change points in time series and point processes - particularly for changes in the mean in time series and for changes in the rate and in the variance in point processes. References - Michael Messer, Marietta Kirchner, Julia Schiemann, Jochen Roeper, Ralph Neininger and Gaby Schneider (2014), A multiple filter test for the detection of rate changes in renewal processes with varying variance <doi:10.1214/14-AOAS782>. Stefan Albert, Michael Messer, Julia Schiemann, Jochen Roeper, Gaby Schneider (2017), Multi-scale detection of variance changes in renewal processes in the presence of rate change points <doi:10.1111/jtsa.12254>. Michael Messer, Kaue M. Costa, Jochen Roeper and Gaby Schneider (2017), Multi-scale detection of rate changes in spike trains with weak dependencies <doi:10.1007/s10827-016-0635-3>. Michael Messer, Stefan Albert and Gaby Schneider (2018), The multiple filter test for change point detection in time series <doi:10.1007/s00184-018-0672-1>. Michael Messer, Hendrik Backhaus, Albrecht Stroh and Gaby Schneider (2019+) Peak detection in time series.
|
2023-06-16 |
|
r-medextractr
|
public |
Function and support for medication and dosing information extraction from free-text clinical notes. Medication entities that can be extracted include drug name, strength, dose amount, dose, frequency, intake time, and time of last dose.
|
2023-06-16 |
|
r-mdimnormn
|
public |
Normalize data to minimize the difference between sample plates (batch effects). For given data in a matrix and grouping variable (or plate), the function 'normn_MA' normalizes the data on MA coordinates. More details are in the citation. The primary method is 'Multi-MA'. Other fitting functions on MA coordinates can also be employed e.g. loess.
|
2023-06-16 |
|
r-matpow
|
public |
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.
|
2023-06-16 |
|
r-managelocalrepo
|
public |
This will allow easier management of a CRAN-style repository on local networks (i.e. not on CRAN). This might be necessary where hosted packages contain intellectual property owned by a corporation.
|
2023-06-16 |
|
r-lsdv
|
public |
Fit a least square dummy variable regression
|
2023-06-16 |
|
r-lrmest
|
public |
When multicollinearity exists among predictor variables of the linear model, least square estimators does not provide a better solution for estimating parameters. To deal with multicollinearity several estimators are proposed in the literature. Some of these estimators are Ordinary Least Square Estimator (OLSE), Ordinary Generalized Ordinary Least Square Estimator (OGOLSE), Ordinary Ridge Regression Estimator (ORRE), Ordinary Generalized Ridge Regression Estimator (OGRRE), Restricted Least Square Estimator (RLSE), Ordinary Generalized Restricted Least Square Estimator (OGRLSE), Ordinary Mixed Regression Estimator (OMRE), Ordinary Generalized Mixed Regression Estimator (OGMRE), Liu Estimator (LE), Ordinary Generalized Liu Estimator (OGLE), Restricted Liu Estimator (RLE), Ordinary Generalized Restricted Liu Estimator (OGRLE), Stochastic Restricted Liu Estimator (SRLE), Ordinary Generalized Stochastic Restricted Liu Estimator (OGSRLE), Type (1),(2),(3) Liu Estimator (Type-1,2,3 LTE), Ordinary Generalized Type (1),(2),(3) Liu Estimator (Type-1,2,3 OGLTE), Type (1),(2),(3) Adjusted Liu Estimator (Type-1,2,3 ALTE), Ordinary Generalized Type (1),(2),(3) Adjusted Liu Estimator (Type-1,2,3 OGALTE), Almost Unbiased Ridge Estimator (AURE), Ordinary Generalized Almost Unbiased Ridge Estimator (OGAURE), Almost Unbiased Liu Estimator (AULE), Ordinary Generalized Almost Unbiased Liu Estimator (OGAULE), Stochastic Restricted Ridge Estimator (SRRE), Ordinary Generalized Stochastic Restricted Ridge Estimator (OGSRRE), Restricted Ridge Regression Estimator (RRRE) and Ordinary Generalized Restricted Ridge Regression Estimator (OGRRRE). To select the best estimator in a practical situation the Mean Square Error (MSE) is used. Using this package scalar MSE value of all the above estimators and Prediction Sum of Square (PRESS) values of some of the estimators can be obtained, and the variation of the MSE and PRESS values for the relevant estimators can be shown graphically.
|
2023-06-16 |
|
r-lrgs
|
public |
Implements a Gibbs sampler to do linear regression with multiple covariates, multiple responses, Gaussian measurement errors on covariates and responses, Gaussian intrinsic scatter, and a covariate prior distribution which is given by either a Gaussian mixture of specified size or a Dirichlet process with a Gaussian base distribution.
|
2023-06-16 |
|
r-lpint
|
public |
Estimates the intensity function, or its derivative of a given order, of a multiplicative counting process using the local polynomial method
|
2023-06-16 |
|
r-logranka
|
public |
LogrankA provides a logrank test across unlimited groups with the possibility to input aggregated survival data.
|
2023-06-16 |
|
r-linprog
|
public |
This package can be used to solve Linear Programming / Linear Optimization problems by using the simplex algorithm.
|
2023-06-16 |
|
r-lexiconpt
|
public |
Provides easy access for sentiment lexicons for those who want to do text analysis in Portuguese texts. As of now, two Portuguese lexicons are available: 'SentiLex-PT02' and 'OpLexicon' (v2.1 and v3.0).
|
2023-06-16 |
|
r-leanpubr
|
public |
Provides access to the 'Leanpub' API <https://leanpub.com/help/api> for gathering information about publications and submissions to the 'Leanpub' platform.
|
2023-06-16 |
|
r-ldlinkr
|
public |
Provides access to the LDlink API (<https://ldlink.nci.nih.gov/?tab=apiaccess>) using the R console. This programmatic access facilitates researchers who are interested in performing batch queries in 1000 Genomes Project data using LDlink.
|
2023-06-16 |
|
r-ldrtools
|
public |
Linear dimension reduction subspaces can be uniquely defined using orthogonal projection matrices. This package provides tools to compute distances between such subspaces and to compute the average subspace. For details see Liski, E.Nordhausen K., Oja H., Ruiz-Gazen A. (2016) Combining Linear Dimension Reduction Subspaces <doi:10.1007/978-81-322-3643-6_7>.
|
2023-06-16 |
|
r-learnbayes
|
public |
A collection of functions helpful in learning the basic tenets of Bayesian statistical inference. It contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions. It contains MCMC algorithms for summarizing posterior distributions defined by the user. It also contains functions for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.
|
2023-06-16 |
|
r-linlir
|
public |
This package implements the methodology of Likelihood-based Imprecise Regression (LIR) for the case of linear regression with interval data.
|
2023-06-16 |
|
r-leaflet.opacity
|
public |
Extends the 'leaflet' R package with the 'Leaflet.OpacityControls' JavaScript plugin. Adds controls to the leaflet map for adjusting the opacity of a layer.
|
2023-06-16 |
