R Development Page
Contributed R Packages
Below is a list of all packages provided by project CloneSeeker.
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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CloneData | Data to Support CloneSeeker Algorithm
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This is a data package to provide simulated example data for
the CloneSeeker package, which implements an algorithm to determine
clonal architecture from SNP-array copy number data, sequencing
mutation data, or both. See Zucker and colleagues (2019)
. |
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Version: 1.0.5 |
Last change: 2022-06-30 18:55:27+02 |
Rev.: 162 |
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Download:
 (.tar.gz) |
 (.zip) |
Build status: Current |
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R install command:
install.packages("CloneData", repos="http://R-Forge.R-project.org") |
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CloneSeeker | Seeking and Finding Clones in Copy Number and Sequencing Data
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Defines the classes and functions used to simulate and
to analyze data sets describing copy number variants and,
optionally, sequencing mutations in order to detect clonal subsets.
See Zucker et al. (2019) . |
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Version: 1.0.13 |
Last change: 2025-04-08 18:00:44+02 |
Rev.: 177 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Current | Stable Release: Get CloneSeeker 1.0.13 from CRAN |
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R install command:
install.packages("CloneSeeker", repos="http://R-Forge.R-project.org") |
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SVAlignR | Recovering Structure of Long Molecules from Structural Variation Data
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Implements a method to combine multiple levels of multiple
sequence alignment to uncover the structure of complex DNA rearrangements. |
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Version: 0.4.6 |
Last change: 2025-04-09 20:11:50+02 |
Rev.: 178 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Current |
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R install command:
install.packages("SVAlignR", repos="http://R-Forge.R-project.org") |
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TACG | Simulating CNV Data
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Provides functions to generate realistic simulations of chromosomes with
CNVs, apply segmentation algorithms to said chromosomes, and assess the accuracy
the results. |
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Version: 1.0.1 |
Last change: 2019-05-28 14:39:56+02 |
Rev.: 142 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Failed to build |
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R install command:
install.packages("TACG", repos="http://R-Forge.R-project.org") |
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Tonto | Testing Viral Integration in 10X Sequencing Data
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Implements a model to decide if 10X linked-read
sequencing data comes from human DNA with an integrated virus or
from episomal fragmented copies of DNA. |
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Version: 0.0.1 |
Last change: 2018-04-30 22:42:51+02 |
Rev.: 79 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Failed to build |
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R install command:
install.packages("Tonto", 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.
3 - Failed to build: the package failed to build or did not pass the checks on the Linux and/or Windows platform. It is not made available since it does not meet the policies.
4 - Conflicts: two or more packages of the same name exist. None of them will be built. Maintainers are asked to negotiate further actions.
5 - Offline: the package is not available. The build system may be offline or the package maintainer did not trigger a rebuild (done e.g., via committing to the package repository).
If your package is not shown on this page or not building, then check the build system status report.
