R Development Page
Contributed R Packages
Below is a list of all packages provided by project OOMPA.
Important note for package
binaries: R-Forge provides these binaries only for
the most recent version of R, but not for older
versions. In order to successfully install the
packages provided on R-Forge, you have to switch
to the most recent version of R or, alternatively,
install from the package sources (.tar.gz).
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BetaModels | Bayesian Analysis of Different Rates in Different Groups
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Test for different proportions (rates) in different groups
using a Bayesian model in which all rate parameters follow a beta
distribution and are selected from a common hyperdistribution. Includes
tools to fit an arbitrary mixture of beta distributions. |
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Version: 0.5.2 |
Last change: 2024-02-08 22:54:22+01 |
Rev.: 641 |
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Download:
 (.tar.gz) |
 (.zip) |
Build status: Current |
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R install command:
install.packages("BetaModels", repos="http://R-Forge.R-project.org") |
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ClassComparison | Classes and Methods for "Class Comparison" Problems on Microarrays
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Defines the classes used for "class comparison" problems
in the OOMPA project (). Class
comparison includes tests for differential expression; see Simons
book for details on typical problem types. |
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Version: 3.2.0 |
Last change: 2023-06-20 19:19:32+02 |
Rev.: 624 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Current | Stable Release: Get ClassComparison 3.1.8 from CRAN |
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R install command:
install.packages("ClassComparison", repos="http://R-Forge.R-project.org") |
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ClassDiscovery | Classes and Methods for "Class Discovery" with Microarrays or Proteomics
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Defines the classes used for "class discovery" problems
in the OOMPA project (). Class
discovery primarily consists of unsupervised clustering methods with
attempts to assess their statistical significance. |
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Version: 3.4.3 |
Last change: 2021-08-04 14:34:09+02 |
Rev.: 483 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Current | Stable Release: Get ClassDiscovery 3.4.0 from CRAN |
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R install command:
install.packages("ClassDiscovery", repos="http://R-Forge.R-project.org") |
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Polychrome | Qualitative Palettes with Many Colors
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Tools for creating, viewing, and assessing qualitative
palettes with many (20-30 or more) colors. See Coombes and colleagues
(2019) . |
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Version: 1.5.1 |
Last change: 2022-04-29 22:13:44+02 |
Rev.: 507 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Current | Stable Release: Get Polychrome 1.5.1 from CRAN |
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R install command:
install.packages("Polychrome", repos="http://R-Forge.R-project.org") |
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PreProcess | Basic Functions for Pre-Processing Microarrays
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Provides classes to pre-process microarray gene
expression data as part of the OOMPA collection of packages
described at . |
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Version: 3.1.7 |
Last change: 2019-05-01 22:30:03+02 |
Rev.: 441 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Current | Stable Release: Get PreProcess 3.1.7 from CRAN |
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R install command:
install.packages("PreProcess", repos="http://R-Forge.R-project.org") |
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TailRank | The Tail-Rank Statistic
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Implements the tail-rank statistic for selecting biomarkers
from a microarray data set, an efficient nonparametric test focused
on the distributional tails. See
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Version: 3.2.3 |
Last change: 2023-01-12 16:45:27+01 |
Rev.: 612 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Current | Stable Release: Get TailRank 3.2.2 from CRAN |
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R install command:
install.packages("TailRank", repos="http://R-Forge.R-project.org") |
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oompaBase | Class Unions, Matrix Operations, and Color Schemes for OOMPA
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Provides the class unions that must be
preloaded in order for the basic tools in the OOMPA (Object-Oriented
Microarray and Proteomics Analysis) project to be defined and loaded.
It also includes vectorized operations for row-by-row means,
variances, and t-tests. Finally, it provides new color schemes.
Details on the packages in the OOMPA project can be found at
. |
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Version: 3.2.9 |
Last change: 2019-08-19 19:48:24+02 |
Rev.: 446 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Current | Stable Release: Get oompaBase 3.2.9 from CRAN |
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R install command:
install.packages("oompaBase", repos="http://R-Forge.R-project.org") |
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oompaData | Data to Illustrate OOMPA Algorithms
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This is a data-only package to provide example data for
other packages that are part of the "Object-Oriented Microrray and
Proteomics Analysis" suite of packages. These are described in more
detail at the package URL. |
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Version: 3.1.3 |
Last change: 2022-12-21 21:53:18+01 |
Rev.: 609 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Current | Stable Release: Get oompaData 3.1.3 from CRAN |
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R install command:
install.packages("oompaData", repos="http://R-Forge.R-project.org") |
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plasma | Partial LeAst Squares for Multiomic Analysis
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Contains tools for supervised analyses of incomplete, overlapping
multiomics datasets. Applies partial least squares in multiple steps to find
models that predict survival outcomes. See Yamaguchi et al. (2023)
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Version: 1.1.2 |
Last change: 2024-01-25 15:09:41+01 |
Rev.: 639 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Current | Stable Release: Get plasma 1.0.0 from CRAN |
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R install command:
install.packages("plasma", repos="http://R-Forge.R-project.org") |
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Build status codes
0 - Current: the package is available for download. The corresponding package passed checks on the Linux and Windows platform without ERRORs.
1 - Scheduled for build: the package has been recognized by the build system and provided in the staging area.
2 - Building: the package has been sent to the build machines. It will be built and checked using the latest patched version of R. Note that it is included in a batch of several packages. Thus, this process will take some time to finish.
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