Showing 39 of total 39 results (show query)
edzer
sp:Classes and Methods for Spatial Data
Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc. From this version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all, see <https://r-spatial.org/r/2023/05/15/evolution4.html> for details.
Maintained by Edzer Pebesma. Last updated 2 months ago.
127 stars 18.63 score 35k scripts 1.3k dependents
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 4 months ago.
geneticsinfrastructuredatarepresentationsequencingannotationgenomeannotationcoveragebioconductor-packagecore-package
44 stars 17.68 score 13k scripts 1.3k dependents
rspatial
terra:Spatial Data Analysis
Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Maintained by Robert J. Hijmans. Last updated 2 days ago.
geospatialrasterspatialvectoronetbbprojgdalgeoscpp
559 stars 17.64 score 17k scripts 855 dependentsrspatial
raster:Geographic Data Analysis and Modeling
Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.
Maintained by Robert J. Hijmans. Last updated 11 hours ago.
163 stars 17.23 score 58k scripts 562 dependentsbioc
SummarizedExperiment:A container (S4 class) for matrix-like assays
The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.
Maintained by Hervé Pagès. Last updated 5 months ago.
geneticsinfrastructuresequencingannotationcoveragegenomeannotationbioconductor-packagecore-package
34 stars 16.84 score 8.6k scripts 1.2k dependentsbioc
GenomeInfoDb:Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.
Maintained by Hervé Pagès. Last updated 2 months ago.
geneticsdatarepresentationannotationgenomeannotationbioconductor-packagecore-package
32 stars 16.32 score 1.3k scripts 1.7k 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
S4Vectors:Foundation of vector-like and list-like containers in Bioconductor
The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).
Maintained by Hervé Pagès. Last updated 2 months ago.
infrastructuredatarepresentationbioconductor-packagecore-package
18 stars 16.05 score 1.0k scripts 1.9k dependents
rstudio
config:Manage Environment Specific Configuration Values
Manage configuration values across multiple environments (e.g. development, test, production). Read values using a function that determines the current environment and returns the appropriate value.
Maintained by Andrie de Vries. Last updated 3 months ago.
261 stars 15.69 score 1.8k scripts 202 dependents
mhahsler
arules:Mining Association Rules and Frequent Itemsets
Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). Also provides C implementations of the association mining algorithms Apriori and Eclat. Hahsler, Gruen and Hornik (2005) <doi:10.18637/jss.v014.i15>.
Maintained by Michael Hahsler. Last updated 2 months ago.
arulesassociation-rulesfrequent-itemsets
194 stars 13.99 score 3.3k scripts 28 dependents
ropensci
git2r:Provides Access to Git Repositories
Interface to the 'libgit2' library, which is a pure C implementation of the 'Git' core methods. Provides access to 'Git' repositories to extract data and running some basic 'Git' commands.
Maintained by Stefan Widgren. Last updated 9 hours ago.
gitgit-clientlibgit2libgit2-library
218 stars 13.93 score 836 scripts 46 dependents
melff
memisc:Management of Survey Data and Presentation of Analysis Results
An infrastructure for the management of survey data including value labels, definable missing values, recoding of variables, production of code books, and import of (subsets of) 'SPSS' and 'Stata' files is provided. Further, the package allows to produce tables and data frames of arbitrary descriptive statistics and (almost) publication-ready tables of regression model estimates, which can be exported to 'LaTeX' and HTML.
Maintained by Martin Elff. Last updated 23 days ago.
46 stars 12.34 score 1.2k scripts 13 dependents
eddelbuettel
RProtoBuf:R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
Protocol Buffers are a way of encoding structured data in an efficient yet extensible format. Google uses Protocol Buffers for almost all of its internal 'RPC' protocols and file formats. Additional documentation is available in two included vignettes one of which corresponds to our 'JSS' paper (2016, <doi:10.18637/jss.v071.i02>. A sufficiently recent version of 'Protocol Buffers' library is required; currently version 3.3.0 from 2017 is the stated minimum.
Maintained by Dirk Eddelbuettel. Last updated 12 days ago.
c-plus-plusprotocol-buffersprotobufcpp
73 stars 11.44 score 126 scripts 21 dependents
flr
FLCore:Core Package of FLR, Fisheries Modelling in R
Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flr-project.org/>.
Maintained by Iago Mosqueira. Last updated 8 days ago.
fisheriesflrfisheries-modelling
16 stars 8.78 score 956 scripts 23 dependents
r-hyperspec
hyperSpec:Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)
Comfortable ways to work with hyperspectral data sets, i.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra. The spectra can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f(wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.
Maintained by Claudia Beleites. Last updated 10 months ago.
data-wranglinghyperspectralimaginginfrarednmrramanspectroscopyuv-visxrf
16 stars 8.10 score 233 scripts 2 dependents
polmine
polmineR:Verbs and Nouns for Corpus Analysis
Package for corpus analysis using the Corpus Workbench ('CWB', <https://cwb.sourceforge.io>) as an efficient back end for indexing and querying large corpora. The package offers functionality to flexibly create subcorpora and to carry out basic statistical operations (count, co-occurrences etc.). The original full text of documents can be reconstructed and inspected at any time. Beyond that, the package is intended to serve as an interface to packages implementing advanced statistical procedures. Respective data structures (document-term matrices, term-co-occurrence matrices etc.) can be created based on the indexed corpora.
Maintained by Andreas Blaette. Last updated 1 years ago.
49 stars 7.96 score 311 scripts
cran
timeSeries:Financial Time Series Objects (Rmetrics)
'S4' classes and various tools for financial time series: Basic functions such as scaling and sorting, subsetting, mathematical operations and statistical functions.
Maintained by Georgi N. Boshnakov. Last updated 6 months ago.
2 stars 7.89 score 146 dependents
adamlilith
fasterRaster:Faster Raster and Spatial Vector Processing Using 'GRASS GIS'
Processing of large-in-memory/large-on disk rasters and spatial vectors using 'GRASS GIS' <https://grass.osgeo.org/>. Most functions in the 'terra' package are recreated. Processing of medium-sized and smaller spatial objects will nearly always be faster using 'terra' or 'sf', but for large-in-memory/large-on-disk objects, 'fasterRaster' may be faster. To use most of the functions, you must have the stand-alone version (not the 'OSGeoW4' installer version) of 'GRASS GIS' 8.0 or higher.
Maintained by Adam B. Smith. Last updated 2 days ago.
aspectdistancefragmentationfragmentation-indicesgisgrassgrass-gisrasterraster-projectionrasterizeslopetopographyvectorization
57 stars 7.68 score 8 scripts
argocanada
argoFloats:Analysis of Oceanographic Argo Floats
Supports the analysis of oceanographic data recorded by Argo autonomous drifting profiling floats. Functions are provided to (a) download and cache data files, (b) subset data in various ways, (c) handle quality-control flags and (d) plot the results according to oceanographic conventions. A shiny app is provided for easy exploration of datasets. The package is designed to work well with the 'oce' package, providing a wide range of processing capabilities that are particular to oceanographic analysis. See Kelley, Harbin, and Richards (2021) <doi:10.3389/fmars.2021.635922> for more on the scientific context and applications.
Maintained by Dan Kelley. Last updated 1 months ago.
17 stars 7.32 score 203 scriptsbioc
TnT:Interactive Visualization for Genomic Features
A R interface to the TnT javascript library (https://github.com/ tntvis) to provide interactive and flexible visualization of track-based genomic data.
Maintained by Jialin Ma. Last updated 5 months ago.
infrastructurevisualizationbioconductorgenome-browserhtmlwidgetsshiny
14 stars 7.15 score 17 scriptsflr
mse:Tools for Running Management Strategy Evaluations using FLR
A set of functions and methods to enable the development and running of Management Strategy Evaluation (MSE) analyses, using the FLR packages and classes and the a4a methods and algorithms.
Maintained by Iago Mosqueira. Last updated 1 months ago.
4 stars 6.99 score 137 scripts 3 dependentsflr
FLasher:Projection and Forecasting of Fish Populations, Stocks and Fleets
Projection of future population and fishery dynamics is carried out for a given set of management targets. A system of equations is solved, using Automatic Differentation (AD), for the levels of effort by fishery (fleet) that will result in the required abundances, catches or fishing mortalities.
Maintained by Iago Mosqueira. Last updated 21 days ago.
2 stars 6.86 score 254 scripts 6 dependents
randrescastaneda
joyn:Tool for Diagnosis of Tables Joins and Complementary Join Features
Tool for diagnosing table joins. It combines the speed of `collapse` and `data.table`, the flexibility of `dplyr`, and the diagnosis and features of the `merge` command in `Stata`.
Maintained by R.Andres Castaneda. Last updated 3 months ago.
9 stars 6.83 score 31 scripts
toxpi
toxpiR:Create ToxPi Prioritization Models
Enables users to build 'ToxPi' prioritization models and provides functionality within the grid framework for plotting ToxPi graphs. 'toxpiR' allows for more customization than the 'ToxPi GUI' (<https://toxpi.org>) and integration into existing workflows for greater ease-of-use, reproducibility, and transparency. toxpiR package behaves nearly identically to the GUI; the package documentation includes notes about all differences. The vignettes download example files from <https://github.com/ToxPi/ToxPi-example-files>.
Maintained by Jonathon F Fleming. Last updated 7 months ago.
data-sciencemodelingtoxicology
11 stars 6.58 score 19 scripts
rickhelmus
patRoon:Workflows for Mass-Spectrometry Based Non-Target Analysis
Provides an easy-to-use interface to a mass spectrometry based non-target analysis workflow. Various (open-source) tools are combined which provide algorithms for extraction and grouping of features, extraction of MS and MS/MS data, automatic formula and compound annotation and grouping related features to components. In addition, various tools are provided for e.g. data preparation and cleanup, plotting results and automatic reporting.
Maintained by Rick Helmus. Last updated 7 days ago.
mass-spectrometrynon-targetcppopenjdk
65 stars 6.24 score 43 scriptsbioc
HiContacts:Analysing cool files in R with HiContacts
HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.
Maintained by Jacques Serizay. Last updated 10 days ago.
12 stars 6.07 score 49 scripts
frankkramer-lab
mully:Create, Modify and Visualize Multi-Layered Networks
Allows the user to create graphs with multiple layers. The user can also modify the layers, the nodes, and the edges. The graph can also be visualized. Zaynab Hammoud and Frank Kramer (2018) <doi:10.3390/genes9110519>. More about multilayered graphs and their usage can be found in our review paper: Zaynab Hammoud and Frank Kramer (2020) <doi:10.1186/s41044-020-00046-0>.
Maintained by Zaynab Hammoud. Last updated 2 years ago.
big-networksdata-visualizationgraph-theorygraphsigraphmultilayer-networksnode-colored-graphs
45 stars 5.95 score 6 scripts
fdetsch
Orcs:Omnidirectional R Code Snippets
I tend to repeat the same code chunks over and over again. At first, this was fine for me and I paid little attention to such redundancies. A little later, when I got tired of manually replacing Linux filepaths with the referring Windows versions, and vice versa, I started to stuff some very frequently used work-steps into functions and, even later, into a proper R package. And that's what this package is - a hodgepodge of various R functions meant to simplify (my) everyday-life coding work without, at the same time, being devoted to a particular scope of application.
Maintained by Florian Detsch. Last updated 2 years ago.
5 stars 5.87 score 98 scripts
iqis
Q7:Types and Features for Object Oriented Programming
Construct message-passing style objects with types and features. Q7 types uses composition instead of inheritance in creating derived types, allowing definining any code segment as feature and associating any feature to any object. Compared to R6, Q7 is simpler, more flexible, and more friendly.
Maintained by Siqi Zhang. Last updated 3 years ago.
5 stars 5.10 score 10 scriptsbioc
ReadqPCR:Read qPCR data
The package provides functions to read raw RT-qPCR data of different platforms.
Maintained by James Perkins. Last updated 5 months ago.
dataimportmicrotitreplateassaygeneexpressionqpcr
5.01 score 17 scripts 1 dependents
pchausse
momentfit:Methods of Moments
Several classes for moment-based models are defined. The classes are defined for moment conditions derived from a single equation or a system of equations. The conditions can also be expressed as functions or formulas. Several methods are also offered to facilitate the development of different estimation techniques. The methods that are currently provided are the Generalized method of moments (Hansen 1982; <doi:10.2307/1912775>), for single equations and systems of equation, and the Generalized Empirical Likelihood (Smith 1997; <doi:10.1111/j.0013-0133.1997.174.x>, Kitamura 1997; <doi:10.1214/aos/1069362388>, Newey and Smith 2004; <doi:10.1111/j.1468-0262.2004.00482.x>, and Anatolyev 2005 <doi:10.1111/j.1468-0262.2005.00601.x>).
Maintained by Pierre Chausse. Last updated 1 years ago.
4.80 score 21 scripts 1 dependentsflr
FLAssess:Generic Classes and Methods for Stock Assessment Models
A generic set of classes for stock assessment models are provided here. Individual assessment packages should extend the basic classes.
Maintained by Iago Mosqueira. Last updated 4 months ago.
4.77 score 324 scripts 3 dependents
cdueben
cppcontainers:'C++' Standard Template Library Containers
Use 'C++' Standard Template Library containers interactively in R. Includes sets, unordered sets, multisets, unordered multisets, maps, unordered maps, multimaps, unordered multimaps, stacks, queues, priority queues, vectors, deques, forward lists, and lists.
Maintained by Christian Düben. Last updated 2 months ago.
4.70 score 1 scriptsbioc
flowMerge:Cluster Merging for Flow Cytometry Data
Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed.
Maintained by Greg Finak. Last updated 5 months ago.
immunooncologyclusteringflowcytometry
4.56 score 6 scripts 1 dependentsbioc
PDATK:Pancreatic Ductal Adenocarcinoma Tool-Kit
Pancreatic ductal adenocarcinoma (PDA) has a relatively poor prognosis and is one of the most lethal cancers. Molecular classification of gene expression profiles holds the potential to identify meaningful subtypes which can inform therapeutic strategy in the clinical setting. The Pancreatic Cancer Adenocarcinoma Tool-Kit (PDATK) provides an S4 class-based interface for performing unsupervised subtype discovery, cross-cohort meta-clustering, gene-expression-based classification, and subsequent survival analysis to identify prognostically useful subtypes in pancreatic cancer and beyond. Two novel methods, Consensus Subtypes in Pancreatic Cancer (CSPC) and Pancreatic Cancer Overall Survival Predictor (PCOSP) are included for consensus-based meta-clustering and overall-survival prediction, respectively. Additionally, four published subtype classifiers and three published prognostic gene signatures are included to allow users to easily recreate published results, apply existing classifiers to new data, and benchmark the relative performance of new methods. The use of existing Bioconductor classes as input to all PDATK classes and methods enables integration with existing Bioconductor datasets, including the 21 pancreatic cancer patient cohorts available in the MetaGxPancreas data package. PDATK has been used to replicate results from Sandhu et al (2019) [https://doi.org/10.1200/cci.18.00102] and an additional paper is in the works using CSPC to validate subtypes from the included published classifiers, both of which use the data available in MetaGxPancreas. The inclusion of subtype centroids and prognostic gene signatures from these and other publications will enable researchers and clinicians to classify novel patient gene expression data, allowing the direct clinical application of the classifiers included in PDATK. Overall, PDATK provides a rich set of tools to identify and validate useful prognostic and molecular subtypes based on gene-expression data, benchmark new classifiers against existing ones, and apply discovered classifiers on novel patient data to inform clinical decision making.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
geneexpressionpharmacogeneticspharmacogenomicssoftwareclassificationsurvivalclusteringgeneprediction
1 stars 4.31 score 17 scriptsbioc
IWTomics:Interval-Wise Testing for Omics Data
Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.
Maintained by Marzia A Cremona. Last updated 5 months ago.
statisticalmethodmultiplecomparisondifferentialexpressiondifferentialmethylationdifferentialpeakcallinggenomeannotationdataimport
3.30 score 5 scripts
raymondlagonigro
AQuadtree:Confidentiality of Spatial Point Data
Provides an automatic aggregation tool to manage point data privacy, intended to be helpful for the production of official spatial data and for researchers. The package pursues the data accuracy at the smallest possible areas preventing individual information disclosure. The methodology, based on hierarchical geographic data structures performs aggregation and local suppression of point data to ensure privacy as described in Lagonigro, R., Oller, R., Martori J.C. (2017) <doi:10.2436/20.8080.02.55>. The data structures are created following the guidelines for grid datasets from the European Forum for Geography and Statistics.
Maintained by Raymond Lagonigro. Last updated 2 years ago.
2.00 score 5 scriptscran
gstsm:Generalized Spatial-Time Sequence Miner
Implementations of the algorithms present article Generalized Spatial-Time Sequence Miner, original title (Castro, Antonio; Borges, Heraldo ; Pacitti, Esther ; Porto, Fabio ; Coutinho, Rafaelli ; Ogasawara, Eduardo . Generalização de Mineração de Sequências Restritas no Espaço e no Tempo. In: XXXVI SBBD - Simpósio Brasileiro de Banco de Dados, 2021 <doi:10.5753/sbbd.2021.17891>).
Maintained by Antonio Castro. Last updated 2 years ago.
1.70 score