OOMPA
Object-Oriented Massive data Profiling Analysis
OOMPA is a suite of R packages for the analysis of gene expression (RNA), proteomics profiling, and other high throughput molecular biology data. The oriingla acronym stood for "Object Oriented Microarray and Proteomics Analysis". But, like the CAMDA competition run by Duke University, we eventually decided to replace the "Microarrays" in the name with "Massice data" as the technology-of-the-day changes.
OOMPA uses S4 classes to construct object-oriented tools with a consistent user interface. All higher level analysis tools in OOMPA are compatible with the eSet classes defined in BioConductor. The lower level processing tools offer an alternative to parts of BioConductor, but can also be used to enhance existing BioConductor packages.
OOMPA has been a project of the Coombes Lab since at least 2010
Project Overview
The following diagram shows the dependency relationships between the OOMPA
packages. Black arrows indicate dependendencies reflected by
imports. Blue arrows come from Depends
entries in the package DESCRIPTION file. Red arrows indicate a weaker
relationship, reflected by a Suggests entry in the
packager DESCRFIPTION file.
An R-Forge "project" (which is where these started, though they have recently moved to GitLab) can contain multiple packages. We have taken advantage of this structure to organize different packages into different projects. The colors used in the figure indicate the R-Forge or git project; more details about this organization can be found in the Source Code section below. Packages in orange exist in their own "standalone" project. Packages in gray do not live anywhere in the cloud, residing instead in the precarious depths of my personal computer. Packages outlined in magents have not yet been submitted to CRAN, but can be accessed from the appropriate git project.
Installation
Most OOMPA packages have already been submitted to and accepted by CRAN. So, the simplest way to install these packages is to use the standard R facilities (i.e., install.packages) to install R packages along with their dependencies.
Some packages are still only present on GitLab. To install these packages, you can execute the following command for the appropriate "PKGNAME" in "PROJ":
library(remotes)
install.packages("krcoombes/PROJ", "pkg/PKGNAME")
As a specific exmaple, here is the command to install the
oompaBase package from the oompa project, ypu would
type:
install.packages("krcoombes/oompa", "pkg/oompaBase")
(The file structure is left over from the default setup on R-Forge.) More detailed information is provided below to indicate which packages are already present in CRAN and which packages can still only be found on GitLab. A handful of packages listed here still exist only on a local hard drive, having not yet reached a development state where they are ready to be moved onto R-Forge. Their status will be updated here as appropriate.
Support
Source Code
The source packages for OOMPA are available from R-Forge. To simplify package maintenance, the packages are separated into multiple projects. The projects are color-coded in the figure above and in the table below.
| Project Name | Project URL | Project Details |
|---|---|---|
| OOMPA | https://gitlab.com/krcoombes/oompa | OOMPA Packages |
| Class Prediction | https://gitlab.com/krcoombes/classpred | Classpred Packages |
| Thresher | https://gitlab.com/krcoombes/thresherpkg | Thresher Packages |
| Cytangle | https://gitlab.com/krcoombes/cytanglepkg | Cytangle Packages |
| CloneFinder | https://gitlab.com/krcoombes/clonefinderpkg | CloneFinder Packages |
| NameNeedle | https://gitlab.com/krcoombes/nameneedle | NameNeedle |
| SIBER | https://gitlab.com/krcoombes/siber | SIBER |
| integIRTy | https://gitlab.com/krcoombes/integirty | integIRTy |
| UMPIRE | https://gitlab.com/krcoombes/umpire | Umpire |
| NewmanOmics | https://gitlab.com/krcoombes/newmanomics | NewmanOmics |
| NewmanOmics | https://gitlab.com/krcoombes/deepcnv | DeepCNV |
| drexplorer | Available from GitHub | |
| ArrayCube | Under Development | |
| FirstSign | Under Development | |
| CRAAC | Under Development | |
| AccuPloidy | Under Development |
License
Licenses for individual packages vary, so you should see their DESCRIPTION files for details. Most current packages are released under Version 2.0 of the Apache License. Older versions of many other packages, are released under Version 2.0 of the Perl Artistic License.
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