Gabriel Becker

Gabriel Becker

10 packages on CRAN

2 packages on Bioconductor

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Tools for analyzing R expressions or blocks of code and determining the dependencies between them. It focuses on R scripts, but can be used on the bodies of functions. There are many facilities including the ability to summarize or get a high-level view of code, determining dependencies between variables, code improvement suggestions.

fastdigest

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Provides an R interface to Bob Jenkin's streaming, non-cryptographic 'SpookyHash' hash algorithm for use in digest-based comparisons of R objects. 'fastdigest' plugs directly into R's internal serialization machinery, allowing digests of all R objects the serialize() function supports, including reference-style objects via custom hooks. Speed is high and scales linearly by object size; memory usage is constant and negligible.

GRANBase

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Repository based tools for department and analysis level reproducibility. 'GRANBase' allows creation of custom branched, continuous integration-ready R repositories, including incremental testing of only packages which have changed versions since the last repository build.

GRANCore

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Provides the classes and methods for GRANRepository objects that are used within the 'GRAN' build framework for R packages. This is primarily used by the 'GRANBase' package and repositories that are created by it.

histry

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Automatically tracks and makes programmatically available code evaluation history in R sessions and dynamic documents.

genbankr

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Reads Genbank files.

roprov

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A suite of classes and methods which provide low-level support for modeling provenance between in-memory R objects. This is an infrastructure package and is not intended to be used directly by end-users.

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This package provides an implementation of the QuadTree data structure. It uses this to implement fast k-Nearest Neighbor and Rectangular range lookups in 2 dimenions. The primary target is high performance interactive graphics.

switchr

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Provides an abstraction for managing, installing, and switching between sets of installed R packages. This allows users to maintain multiple package libraries simultaneously, e.g. to maintain strict, package-version-specific reproducibility of many analyses, or work within a development/production release paradigm. Introduces a generalized package installation process which supports multiple repository and non-repository sources and tracks package provenance.

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Provides a simple plugin to the switchr framework which allows users to publish package and session manifests as gists.

trackr

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Automatically annotates R-based artifacts with relevant descriptive and provenance-related and provides a backend-agnostic storage and discoverability system for organizing, retrieving, and interrogating such artifacts.

ReportingTools

bioconductor
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The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser. For more examples, please visit our site: http:// research-pub.gene.com/ReportingTools.