This package was removed from CRAN on 2024-11-06. Its history is shown below.

Reason: issues were not corrected in time

Details below reflect version 0.2.2, its last release before removal.

MOSS

0.2.2

Multi-Omic Integration via Sparse Singular Value Decomposition

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Agustin Gonzalez-Reymundez3 releasesCRAN page ↗GitHub ↗

High dimensionality, noise and heterogeneity among samples and features challenge the omic integration task. Here we present an omic integration method based on sparse singular value decomposition (SVD) to deal with these limitations, by: a. obtaining the main axes of variation of the combined omics, b. imposing sparsity constraints at both subjects (rows) and features (columns) levels using Elastic Net type of shrinkage, and c. allowing both linear and non-linear projections (via t-Stochastic Neighbor Embedding) of the omic data to detect clusters in very convoluted data (Gonzalez-Reymundez et. al, 2022) doi:10.1093/bioinformatics/btac179.

Install

R (source archive)pak (dev)Ubuntu (r2u)openSUSE (OBS)

url <- "https://cran.r-project.org/src/contrib/Archive/MOSS/MOSS_0.2.2.tar.gz"
pkgFile <- "MOSS_0.2.2.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.2.2) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("agugonrey/MOSS")

Development version from agugonrey/MOSS. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-moss

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-MOSS

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

CRAN check results are not tracked yet.

Documentation

Documentation signals are not tracked yet for this package.

Downloads

MOSS Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on157 r2u29 autocran22 c2d4u

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (4)

clusterdbscan Rtsnestats

LinkingTo (0)

none

Suggests (21)

annotate bigparallelr bigstatsr future.apply scatterpie clValid ComplexHeatmap fpc ggplot2 ggpmisc ggthemes gridExtra irlba knitrMASSrmarkdown testthat viridis spelling VennDiagramgrid

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Agustin Gonzalez-Reymundez

Author, Maintainer, Copyright holder

Authors (2)

Agustin Gonzalez-Reymundez

Author, Maintainer, Copyright holder

Alexander Grueneberg

Author

Contributors (1)

Ana Vazquez

Contributor, Thesis advisor

Agustin Gonzalez-Reymundez

Author, Maintainer, Copyright holder

Package Timeline

3 releases. R releases are shown for context.

R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2024-11-06
issues were not corrected in time
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.2.2
2022-03-25 · diff ↗
0.2.0
2021-07-16 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.0
2021-01-19
R
R 4.0.0 released · 2020-04-24

Package metadata

Total releases: 3
License: GPL-2 OSI
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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