ggbio - Visualization tools for genomic data
The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.
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infrastructurevisualization
11.79 score 117 stars 19 dependents 904 scripts 5.7k downloadsrtracklayer - R interface to genome annotation files and the UCSC genome browser
Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
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annotationvisualizationdataimportzlibopensslcurl
10.78 score 525 dependents 72 scripts 59k downloadsrestfulr - R Interface to RESTful Web Services
Models a RESTful service as if it were a nested R list.
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7.37 score 2 stars 584 dependents 12 scripts 55k downloadsbiovizBase - Basic graphic utilities for visualization of genomic data.
The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.
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infrastructurevisualizationpreprocessing
6.68 score 68 dependents 2 scripts 12k downloadsgmapR - An R interface to the GMAP/GSNAP/GSTRUCT suite
GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.
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alignmentzlib
4.97 score 93 scripts 504 downloadsrsbml - R support for SBML, using libsbml
Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models.
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graphandnetworkpathwaysnetworklibsbmlcpp
4.37 score 26 scriptsplumbr - Mutable and dynamic data models
The base R data.frame, like any vector, is copied upon modification. This behavior is at odds with that of GUIs and interactive graphics. To rectify this, plumbr provides a mutable, dynamic tabular data model. Models may be chained together to form the complex plumbing necessary for sophisticated graphical interfaces. Also included is a general framework for linking datasets; an typical use case would be a linked brush.
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4.18 score 18 stars 28 scripts 270 downloadsVariantToolsData - Data for the VariantTools tutorial
Data from the sequencing of a 50/50 mixture of HapMap trio samples NA12878 (CEU) and NA19240 (YRI), subset to the TP53 region.
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experimentdatasequencingdatahapmapsnpdatadatapkg
3.60 score 1 scriptsmicroRNA - Data and functions for dealing with microRNAs
Different data resources for microRNAs and some functions for manipulating them.
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infrastructuregenomeannotationsequencematchingcpp
3.48 score 1.5k downloadsHelloRangesData - Data for the HelloRanges tutorial vignette
Provides the data that were used in the bedtools tutorial by Aaron Quinlan (http://quinlanlab.org/tutorials/bedtools/bedtools.html). Includes a subset of the DnaseI hypersensitivity data from "Maurano et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195." The rest of the tracks were originally downloaded from the UCSC table browser. See the HelloRanges vignette for a port of the bedtools tutorial to R.
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experimentdatasequencingdatadatapkg
3.30 score 4 scriptsHelloRanges - Introduce *Ranges to bedtools users
Translates bedtools command-line invocations to R code calling functions from the Bioconductor *Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.
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sequencingannotationcoveragegenomeannotationdataimportsequencematchingvariantannotation
3.28 score 1 dependents 32 scripts 724 downloadsLungCancerLines - Reads from Two Lung Cancer Cell Lines
Reads from an RNA-seq experiment between two lung cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as Fastq files and are meant for use with the TP53Genome object in the gmapR package.
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experimentdatagenomecancerdatalungcancerdatarnaseqdatadatapkg
2.88 score 19 scriptsobjectProperties - A Factory of Self-Describing Properties
Supports the definition of sets of properties on objects. Observers can listen to changes on individual properties or the set as a whole. The properties are meant to be fully self-describing. In support of this, there is a framework for defining enumerated types, as well as other bounded types, as S4 classes.
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2.46 score 4 dependents 24 scripts 411 downloadsobjectSignals - Observer Pattern for S4
A mutable Signal object can report changes to its state, clients could register functions so that they are called whenever the signal is emitted. The signal could be emitted, disconnected, blocked, unblocked, and buffered.
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2.26 score 6 dependents 7 scripts 361 downloads