rtracklayer - 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
13.00 score 513 dependents 14k scripts 47k downloadsggbio - 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
12.74 score 116 stars 18 dependents 908 scripts 3.2k 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
8.25 score 73 dependents 445 scripts 9.2k downloadsrestfulr - R Interface to RESTful Web Services
Models a RESTful service as if it were a nested R list.
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7.31 score 2 stars 516 dependents 8 scripts 66k 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
5.12 score 94 scriptsrsolr - R to Solr Interface
A comprehensive R API for querying Apache Solr databases. A Solr core is represented as a data frame or list that supports Solr-side filtering, sorting, transformation and aggregation, all through the familiar base R API. Queries are processed lazily, i.e., a query is only sent to the database when the data are required.
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4.95 score 9 stars 6 scripts 843 downloadsVariantTools - Tools for Exploratory Analysis of Variant Calls
Explore, diagnose, and compare variant calls using filters.
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geneticsgeneticvariabilitysequencing
4.46 score 58 scriptsrsbml - 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
4.32 score 23 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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4.21 score 18 stars 30 scripts 271 downloadsHelloRanges - 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
3.64 score 1 dependents 29 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 7 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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2.39 score 3 dependents 27 scripts 296 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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2.18 score 5 dependents 7 scripts 355 downloads