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readDepth

This package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. In contrast to other published methods, readDepth does not require the sequencing of a reference sample, and uses a robust statistical model that accounts for overdispersed data. It includes a method for effectively increasing the resolution obtained from low-coverage experiments by utilizing breakpoint information from paired end sequencing to do positional refinement. It can also be used to infer copy number using reads obtained from bisulfite sequencing experiments.

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readDepth classification

readDepth specifications

Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
License:
Apache License version 2.0
Stability:
Stable
Interface:
Command line interface
Input format:
BED
Programming languages:
R
Computer skills:
Advanced
Maintained:
Yes

readDepth distribution

versioning

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No versioning.

readDepth support

Documentation

Credits

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Publications

Institution(s)

Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, USA

Link to literature

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