Documentation Scientific and Technical Beat

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BEDtools

BEDTools is a set of utilities allow to one to address common genomics tasks such as finding feature overlaps and computing coverage. BEDtools is new to Fedora.

R

R is a popular statistics package with many add on packages to address specific needs. Fedora 15 brings a few new add-on packages to R.

R-GenomicRanges

R-GenomicRanges provides general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.

http://www.bioconductor.org/packages/release/bioc/html/GenomicRanges.html

R-ROC

The ROC library is a collection of R classes and functions related to receiver operating characteristic (ROC) curves. These functions are targeted at the use of ROC analysis with DNA microarrays The R-ROC package provides a set of utilities for ROC.

http://bioconductor.org/packages/release/bioc/html/ROC.html

R-affydata

R-affydata is a set of example affymetrix datasets. These datasets are somewhat larger than the examples included in the affy package, and are intended to better represent "real-world" datasets.

http://www.bioconductor.org/packages/2.6/data/experiment/html/affydata.html

APE

ape (Atomic Pseudopotential Engine) is a tool for generating atomic pseudopotentials within a Density-Functional Theory framework. It is distributed under the GPL and it produces pseudopotential files suitable for use with