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m2w64-htslib
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public |
C library for high-throughput sequencing data formats.
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2025-03-25 |
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r-archr
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public |
This package is designed to streamline scATAC analyses in R.
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2025-03-25 |
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cross-r-base
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public |
R is a free software environment for statistical computing and graphics.
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2025-03-25 |
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r-base
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public |
R is a free software environment for statistical computing and graphics.
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2025-03-25 |
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r-h2gener
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public |
A method for partitioning gene-level contributions to complex-trait heritability by allele frequency (or any other binary annotations)
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2025-03-25 |
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r-susier
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public |
The package implements a simple new way to perform variable selection in multiple regression ($y=Xb+e$), using computationally efficient variational Bayes approach. The methods implemented here are particularly well-suited to settings where some of the X variables are highly correlated, and the true effects are highly sparse (e.g. <20 non-zero effects in the vector $b$), although it is also useful to more general applications.
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2025-03-25 |
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r-tinier
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public |
Shrink image filesizes with the TinyPNG API <https://tinypng.com>. Works with .png and .jpg/.jpeg files, and can return the new image filepath to enable embedding in other image workflows/functions.
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2025-03-25 |
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r-mixsqp
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public |
Provides optimization algorithms based on sequential quadratic programming (SQP) for maximum likelihood estimation of the mixture proportions in a finite mixture model where the component densities are known. The algorithms are expected to obtain solutions that are at least as accurate as the state-of-the-art MOSEK interior-point solver (called by function "KWDual" in the 'REBayes' package), and they are expected to arrive at solutions more quickly in large data sets. The algorithms are described in Y. Kim, P. Carbonetto, M. Stephens & M. Anitescu (2012) <arXiv:1806.01412>.
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2025-03-25 |
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r-mashr
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public |
Empirical Bayes shrinkage of multivariate effects.
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2025-03-25 |
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r-coga
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public |
Evaluation for density and distribution function of convolution of gamma distributions in R. Two related exact methods and one approximate method are implemented with efficient algorithm and C++ code. A quick guide for choosing correct method and usage of this package is given in package vignette.
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2025-03-25 |
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r-rodbc
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public |
An ODBC database interface.
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2025-03-25 |
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sos-r
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public |
SoS Notebook extension for language R
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2025-03-25 |
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sos-notebook
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public |
Script of Scripts (SoS): an interactive, cross-platform, and cross-language workflow system for reproducible data analysis
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2025-03-25 |
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wand
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public |
Ctypes-based simple MagickWand API binding for Python
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2025-03-25 |
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r-dscrutils
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public |
Various R functions for interacting with and analyzing the results of a Dynamic Statistical Comparison (DSC) experiment.
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2025-03-25 |
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sos
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public |
Script of Scripts (SoS): an interactive, cross-platform, and cross-language workflow system for reproducible data analysis
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2025-03-25 |
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r-vicar
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public |
Implements many methods for accounting for unobserved confounding in linear regression. If control genes are available, then the following methods are implementable: a calibrated version of CATE/RUV4 (vruv4), a Bayesian version of RUV (ruvb), a version of RUV that unifies other versions of RUV (ruv3), and a generalized version of RUV (ruvimpute). If control genes are not available, then MOUTHWASH (mouthwash) and BACKWASH (backwash) are excellent procedures to use as long as only one covariate is of interest.
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2025-03-25 |
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r-seqgendiff
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public |
Modifies/generates RNA-seq data for use in simulations.
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2025-03-25 |
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r-cate
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public |
Provides several methods for factor analysis in high dimension (both n,p >> 1) and methods to adjust for possible confounders in multiple hypothesis testing.
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2025-03-25 |
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r-leapp
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public |
These functions take a gene expression value matrix, a primary covariate vector, an additional known covariates matrix. A two stage analysis is applied to counter the effects of latent variables on the rankings of hypotheses. The estimation and adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). "leapp" is developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved.
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2025-03-25 |
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r-esabcv
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public |
These functions estimate the latent factors of a given matrix, no matter it is high-dimensional or not. It tries to first estimate the number of factors using bi-cross-validation and then estimate the latent factor matrix and the noise variances. For more information about the method, see Art B. Owen and Jingshu Wang 2015 archived article on factor model (http://arxiv.org/abs/1503.03515).
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2025-03-25 |
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r-bfa
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public |
Provides model fitting for several Bayesian factor models including Gaussian, ordinal probit, mixed and semiparametric Gaussian copula factor models under a range of priors.
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2025-03-25 |
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r-genlasso
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public |
This package computes the solution path for generalized lasso problems. Important use cases are the fused lasso over an arbitrary graph, and trend fitting of any given polynomial order. Specialized implementations for the latter two subproblems are given to improve stability and speed.
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2025-03-25 |
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r-corshrink
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public |
Performs adaptive shrinkage of correlation and covariance matrices using a mixture model prior over the Fisher z-transformation of the correlations. A separate shrinkage intensity may be specifiedfor each cell of the correlation or the covariance table.
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2025-03-25 |
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r-rcppziggurat
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public |
The Ziggurat generator for normally distributed random numbers, originally proposed by Marsaglia and Tsang (JSS, 2000), has been improved upon a few times starting with Leong et al (JSS, 2005). This package provides an aggregation in order to compare different implementations. The goal is to provide an 'faster but good enough' alternative for use with R and C++ code.
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2025-03-25 |
