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.

Last updated 6 days ago

annotationvisualizationdataimportzlibopensslcurl

12.66 score 481 dependents 6.7k scripts 43k downloads

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.

Last updated 5 months ago

infrastructurevisualization

12.26 score 111 stars 17 dependents 734 scripts 4.4k downloads

biovizBase - 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.

Last updated 5 months ago

infrastructurevisualizationpreprocessing

8.04 score 75 dependents 273 scripts 8.9k downloads

restfulr - R Interface to RESTful Web Services

Models a RESTful service as if it were a nested R list.

Last updated 3 years ago

6.90 score 2 stars 482 dependents 8 scripts 28k downloads

rsbml - 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.

Last updated 16 days ago

graphandnetworkpathwaysnetworklibsbmlcpp

4.71 score 1 dependents 19 scripts 501 downloads

gmapR - 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.

Last updated 14 days ago

alignmentzlib

4.43 score 45 scripts 382 downloads

plumbr - 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.

Last updated 11 years ago

4.19 score 18 stars 29 scripts 221 downloads

HelloRanges - 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.

Last updated 5 months ago

sequencingannotationcoveragegenomeannotationdataimportsequencematchingvariantannotation

4.19 score 1 dependents 26 scripts 304 downloads

VariantTools - Tools for Exploratory Analysis of Variant Calls

Explore, diagnose, and compare variant calls using filters.

Last updated 5 months ago

geneticsgeneticvariabilitysequencing

4.09 score 41 scripts 452 downloads

rsolr - 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.

Last updated 3 years ago

3.65 score 9 stars 6 scripts 251 downloads

microRNA - Data and functions for dealing with microRNAs

Different data resources for microRNAs and some functions for manipulating them.

Last updated 1 months ago

infrastructuregenomeannotationsequencematchingcpp

3.48 score 7 scripts 466 downloads

objectProperties - 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.

Last updated 3 years ago

2.26 score 3 dependents 20 scripts 408 downloads

objectSignals - 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.

Last updated 3 years ago

2.18 score 5 dependents 7 scripts 356 downloads