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mashr  

Multivariate Adaptive Shrinkage
View on CRAN: Click here


Download and install mashr package within the R console
Install from CRAN:
install.packages("mashr")

Install from Github:
library("remotes")
install_github("cran/mashr")

Install by package version:
library("remotes")
install_version("mashr", "0.2.79")



Attach the package and use:
library("mashr")
Maintained by
Peter Carbonetto
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-06-09
Latest Update: 2022-12-07
Description:
Implements the multivariate adaptive shrinkage (mash) method of Urbut et al (2019) for estimating and testing large numbers of effects in many conditions (or many outcomes). Mash takes an empirical Bayes approach to testing and effect estimation; it estimates patterns of similarity among conditions, then exploits these patterns to improve accuracy of the effect estimates. The core linear algebra is implemented in C++ for fast model fitting and posterior computation.
How to cite:
Peter Carbonetto (2020). mashr: Multivariate Adaptive Shrinkage. R package version 0.2.79, https://cran.r-project.org/web/packages/mashr. Accessed 22 Dec. 2024.
Previous versions and publish date:
0.2.28 (2020-06-09 15:30), 0.2.38 (2020-06-19 07:50), 0.2.50 (2021-05-24 02:10), 0.2.57 (2022-01-25 09:52), 0.2.69 (2022-12-07 22:20)
Other packages that cited mashr R package
View mashr citation profile
Other R packages that mashr depends, imports, suggests or enhances
Complete documentation for mashr
Functions, R codes and Examples using the mashr R package
Some associated functions: bovy_wrapper . calc_lik_matrix . calc_lik_matrix_common_cov . calc_lik_vector . calc_relative_lik_matrix . compute_alt_loglik_from_matrix_and_pi . compute_loglik_from_matrix_and_pi . compute_null_loglik_from_matrix . compute_posterior_matrices . compute_posterior_matrices_common_cov_R . compute_posterior_matrices_general_R . compute_posterior_weights . compute_vloglik_from_matrix_and_pi . contrast_matrix . cov_all_zeros . cov_canonical . cov_ed . cov_equal_effects . cov_first_singleton . cov_flash . cov_from_factors . cov_pca . cov_simple_het . cov_udi . cov_udi_single . estimate_null_correlation_simple . expand_cov . extreme_deconvolution . get_estimated_pi . get_log10bf . get_n_significant_conditions . get_pairwise_sharing . get_pairwise_sharing_from_samples . get_samples . get_significant_results . make_names . mash . mash_1by1 . mash_compute_loglik . mash_compute_posterior_matrices . mash_compute_vloglik . mash_estimate_corr_em . mash_plot_meta . mash_set_data . mash_set_data_contrast . mash_update_data . optimize_pi . posterior_cov . posterior_mean . posterior_mean_matrix . scale_cov . sim_contrast1 . sim_contrast2 . simple_sims . simple_sims2 . teem_wrapper . udi_model_matrix . 
Some associated R codes: RcppExports.R . compute_covs.R . cov_udi.R . data2cov.R . ed.R . est_cor.R . extreme_deconvolution.R . get_functions.R . likelihoods_origdata.R . likelihoods_scaleddata.R . mash.R . matrix_utils.R . opt.R . plots.R . posterior.R . posterior_common_cov.R . posterior_lowmem.R . set_data.R . simulations.R . simulations_contrast.R .  Full mashr package functions and examples
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