Showing 9 of total 9 results (show query)
bioc
GenomicRanges:Representation and manipulation of genomic intervals
The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.
Maintained by Hervé Pagès. Last updated 5 months ago.
geneticsinfrastructuredatarepresentationsequencingannotationgenomeannotationcoveragebioconductor-packagecore-package
44 stars 17.68 score 13k scripts 1.3k dependentsbioc
IRanges:Foundation of integer range manipulation in Bioconductor
Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.
Maintained by Hervé Pagès. Last updated 2 months ago.
infrastructuredatarepresentationbioconductor-packagecore-package
22 stars 16.09 score 2.1k scripts 1.8k dependentsbioc
EBImage:Image processing and analysis toolbox for R
EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.
Maintained by Andrzej Oleś. Last updated 5 months ago.
visualizationbioinformaticsimage-analysisimage-processingcpp
71 stars 12.77 score 1.5k scripts 33 dependents
tiledb-inc
tiledb:Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays
The modern database 'TileDB' introduces a powerful on-disk format for storing and accessing any complex data based on multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations. This package provides the R support.
Maintained by Isaiah Norton. Last updated 2 days ago.
arrayhdfss3storage-managertiledbcpp
108 stars 11.79 score 306 scripts 4 dependents
murrayefford
secr:Spatially Explicit Capture-Recapture
Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Maintained by Murray Efford. Last updated 3 days ago.
3 stars 10.06 score 410 scripts 5 dependents
cran
vcd:Visualizing Categorical Data
Visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was package was originally inspired by the book "Visualizing Categorical Data" by Michael Friendly and is now the main support package for a new book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer (2015).
Maintained by David Meyer. Last updated 6 months ago.
5 stars 8.19 score 87 dependents
ropensci
tiler:Create Geographic and Non-Geographic Map Tiles
Creates geographic map tiles from geospatial map files or non-geographic map tiles from simple image files. This package provides a tile generator function for creating map tile sets for use with packages such as 'leaflet'. In addition to generating map tiles based on a common raster layer source, it also handles the non-geographic edge case, producing map tiles from arbitrary images. These map tiles, which have a non-geographic, simple coordinate reference system (CRS), can also be used with 'leaflet' when applying the simple CRS option. Map tiles can be created from an input file with any of the following extensions: tif, grd and nc for spatial maps and png, jpg and bmp for basic images. This package requires 'Python' and the 'gdal' library for 'Python'. 'Windows' users are recommended to install 'OSGeo4W' (<https://trac.osgeo.org/osgeo4w/>) as an easy way to obtain the required 'gdal' support for 'Python'.
Maintained by Matthew Leonawicz. Last updated 7 months ago.
64 stars 7.78 score 39 scripts 2 dependents
hadley
productplots:Product Plots for R
Framework for visualising tables of counts, proportions and probabilities. The framework is called product plots, alluding to the computation of area as a product of height and width, and the statistical concept of generating a joint distribution from the product of conditional and marginal distributions. The framework, with extensions, is sufficient to encompass over 20 visualisations previously described in fields of statistical graphics and 'infovis', including bar charts, mosaic plots, 'treemaps', equal area plots and fluctuation diagrams.
Maintained by Hadley Wickham. Last updated 6 months ago.
29 stars 7.39 score 74 scripts 6 dependentsbioc
GenomicTuples:Representation and Manipulation of Genomic Tuples
GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.
Maintained by Peter Hickey. Last updated 5 months ago.
infrastructuredatarepresentationsequencingcpp
4 stars 5.48 score 7 scripts