Michael Lawrence

Michael Lawrence

18 packages on CRAN

2 packages on GitHub

14 packages on Bioconductor

RGtk2

cran
96th

Percentile

Facilities in the R language for programming graphical interfaces using Gtk, the Gimp Tool Kit.

95th

Percentile

This device uses Cairo and GTK to draw to the screen, file (png, svg, pdf, and ps) or memory (arbitrary GdkDrawable or Cairo context). The screen device may be embedded into RGtk2 interfaces and supports all interactive features of other graphics devices, including getGraphicsEvent().

rsolr

cran
64th

Percentile

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.

plumbr

cran
47th

Percentile

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.

restfulr

cran
47th

Percentile

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

qtbase

cran
31th

Percentile

Dynamic bindings to the Qt library for calling Qt methods and extending Qt clases from R. Other packages build upon qtbase to provide special-purpose high-level interfaces to specific parts of Qt.

qtpaint

cran
31th

Percentile

Low-level interface to functionality in Qt for efficiently drawing dynamic graphics and handling basic user input.

biovizBase

bioconductor
21th

Percentile

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.

explorase

bioconductor
21th

Percentile

explore and analyze *omics data with R and GGobi

ggbio

bioconductor
21th

Percentile

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.

gmapR

bioconductor
21th

Percentile

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.

LazyList

bioconductor
21th

Percentile

The goal of this package is to enhance the performance and facility of data manipulation by extending the S4Vectors framework in a manner consistent with the canonical R API, while taking advantage of efficient routines hidden in the internals of the Bioconductor infrastructure. More concretely, it introduces a formal notion of data "shape" and generalizes the CompressedList concept from IRanges by pairing a vector with an arbitrary grouping. The object behaves like a list, although the data may remain in their original form. A high-level aggregation API is implemented to most efficiently operate over a specific combination of data type and grouping type.

MutableRanges

bioconductor
21th

Percentile

Extends fundamental data structures in the Bioconductor sequencing stack using reference classes from the methods package.

rsbml

bioconductor
21th

Percentile

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.

rtracklayer

bioconductor
21th

Percentile

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.

VariantTools

bioconductor
21th

Percentile

Tools for detecting, filtering, calling, comparing and plotting variants.

evaluate

cran
99.5th

Percentile

Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.

gWidgets

cran
94th

Percentile

Provides a toolkit-independent API for building interactive GUIs. At least one of the 'gWidgetsXXX packages', such as gWidgetstcltk, needs to be installed. Some icons are on loan from the scigraphica project <http://scigraphica.sourceforge.net>.

93th

Percentile

Port of the gWidgets API to the RGtk2 toolkit.

rggobi

cran
85th

Percentile

A command-line interface to 'GGobi', an interactive and dynamic graphics package. 'Rggobi' complements the graphical user interface of 'GGobi' providing a way to fluidly transition between analysis and exploration, as well as automating common tasks.

commandr

cran
76th

Percentile

An S4 representation of the Command design pattern. The Operation class is a simple implementation using closures and supports forward and reverse (undo) evaluation. The more complicated Protocol framework represents each type of command (or analytical protocol) by a formal S4 class. Commands may be grouped and consecutively executed using the Pipeline class. Example use cases include logging, do/undo, analysis pipelines, GUI actions, parallel processing, etc.

sparkhail

cran
64th

Percentile

'Hail' is an open-source, general-purpose, 'python' based data analysis tool with additional data types and methods for working with genomic data, see <https://hail.is/>. 'Hail' is built to scale and has first-class support for multi-dimensional structured data, like the genomic data in a genome-wide association study (GWAS). 'Hail' is exposed as a 'python' library, using primitives for distributed queries and linear algebra implemented in 'scala', 'spark', and increasingly 'C++'. The 'sparkhail' is an R extension using 'sparklyr' package. The idea is to help R users to use 'hail' functionalities with the well-know 'tidyverse' syntax, see <https://www.tidyverse.org/>.

47th

Percentile

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.

47th

Percentile

A mutable Signal object can report changes to its state, clients could register functions so that they are called whenever the signal is emited. The signal could be emited, disconnected, blocked, unblocked, and buffered.

ProgGUIinR

cran
47th

Percentile

sample code, appendices and functions for the text Programming GUIs in R

ddR

cran
21th

Percentile

Provides distributed data structures and simplifies distributed computing in R.

chipseq

bioconductor
21th

Percentile

Tools for helping process short read data for chipseq experiments

CRISPRseek

bioconductor
21th

Percentile

The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. If GeneRfold and GeneR are installed (http://bioconductor.case.edu/bioconductor/2.8/bioc/html/GeneRfold.html, http://bioc.ism.ac.jp/packages/2.8/bioc/html/GeneR.html), then the minimum free energy and bracket notation of secondary structure of gRNA and gRNA backbone constant region will be included in the summary file. This package leverages Biostrings and BSgenome packages.

GUIDEseq

bioconductor
21th

Percentile

The package implements GUIDE-seq analysis workflow including functions for obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites.

cranvas

github
21th

Percentile

This is an R package as the next generation of GGobi, a software package for interactive and dynamic statistical graphics. It includes most of features in GGobi such as brushing, zooming, panning, identifying and linking, as well as common types of statistical graphics, e.g. bar plot, scatter plot, boxplot, histogram, density plot, spine plot, parallel coordinates plot, mosaic plot, maps, missing value plot, time series plot, tour, scatter plot matrix, hexagons and tiles (color images), etc. Based on the support of several other packages, cranvas aims for speed (from Qt) and flexibility (from R), with the style and design borrowed from ggplot2.

pbdDMAT

cran
21th

Percentile

A set of classes for managing distributed matrices, and a collection of methods for computing linear algebra and statistics. Computation is handled mostly by routines from the 'pbdBASE' package, which itself relies on the 'ScaLAPACK' and 'PBLAS' numerical libraries for distributed computing.

ShortRead

bioconductor
21th

Percentile

This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

plyranges

github
21th

Percentile

A dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessiblity for new Bioconductor users is hopefully increased.

VariantAnnotation

bioconductor
21th

Percentile

Annotate variants, compute amino acid coding changes, predict coding outcomes.