Showing 200 of total 1479 results (show query)
shixiangwang
sigminer:Extract, Analyze and Visualize Mutational Signatures for Genomic Variations
Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2021) <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Steele Christopher D., et al. (2022) <DOI:10.1038/s41586-022-04738-6>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.
Maintained by Shixiang Wang. Last updated 5 months ago.
bayesian-nmfbioinformaticscancer-researchcnvcopynumber-signaturescosmic-signaturesdbseasy-to-useindelmutational-signaturesnmfnmf-extractionsbssignature-extractionsomatic-mutationssomatic-variantsvisualizationcpp
53.0 match 150 stars 9.48 score 123 scripts 2 dependents
kwstat
agridat:Agricultural Datasets
Datasets from books, papers, and websites related to agriculture. Example graphics and analyses are included. Data come from small-plot trials, multi-environment trials, uniformity trials, yield monitors, and more.
Maintained by Kevin Wright. Last updated 28 days ago.
45.5 match 125 stars 11.02 score 1.7k scripts 2 dependents
rstudio
gt:Easily Create Presentation-Ready Display Tables
Build display tables from tabular data with an easy-to-use set of functions. With its progressive approach, we can construct display tables with a cohesive set of table parts. Table values can be formatted using any of the included formatting functions. Footnotes and cell styles can be precisely added through a location targeting system. The way in which 'gt' handles things for you means that you don't often have to worry about the fine details.
Maintained by Richard Iannone. Last updated 11 days ago.
docxeasy-to-usehtmllatexrtfsummary-tables
25.3 match 2.1k stars 18.36 score 20k scripts 112 dependents
valentint
rrcov:Scalable Robust Estimators with High Breakdown Point
Robust Location and Scatter Estimation and Robust Multivariate Analysis with High Breakdown Point: principal component analysis (Filzmoser and Todorov (2013), <doi:10.1016/j.ins.2012.10.017>), linear and quadratic discriminant analysis (Todorov and Pires (2007)), multivariate tests (Todorov and Filzmoser (2010) <doi:10.1016/j.csda.2009.08.015>), outlier detection (Todorov et al. (2010) <doi:10.1007/s11634-010-0075-2>). See also Todorov and Filzmoser (2009) <urn:isbn:978-3838108148>, Todorov and Filzmoser (2010) <doi:10.18637/jss.v032.i03> and Boudt et al. (2019) <doi:10.1007/s11222-019-09869-x>.
Maintained by Valentin Todorov. Last updated 7 months ago.
39.3 match 2 stars 10.57 score 484 scripts 96 dependents
mazamascience
MazamaLocationUtils:Manage Spatial Metadata for Known Locations
Utility functions for discovering and managing metadata associated with spatially unique "known locations". Applications include all fields of environmental monitoring (e.g. air and water quality) where data are collected at stationary sites.
Maintained by Jonathan Callahan. Last updated 3 months ago.
71.2 match 5.64 score 108 scripts
davidgohel
officer:Manipulation of Microsoft Word and PowerPoint Documents
Access and manipulate 'Microsoft Word', 'RTF' and 'Microsoft PowerPoint' documents from R. The package focuses on tabular and graphical reporting from R; it also provides two functions that let users get document content into data objects. A set of functions lets add and remove images, tables and paragraphs of text in new or existing documents. The package does not require any installation of Microsoft products to be able to write Microsoft files.
Maintained by David Gohel. Last updated 1 months ago.
ms-office-documentspowerpointword
22.8 match 630 stars 15.79 score 4.1k scripts 137 dependents
bart1
move:Visualizing and Analyzing Animal Track Data
Contains functions to access movement data stored in 'movebank.org' as well as tools to visualize and statistically analyze animal movement data, among others functions to calculate dynamic Brownian Bridge Movement Models. Move helps addressing movement ecology questions.
Maintained by Bart Kranstauber. Last updated 4 months ago.
26.9 match 8.74 score 690 scripts 3 dependents
fishr-core-team
FSAdata:Data to Support Fish Stock Assessment ('FSA') Package
The datasets to support the Fish Stock Assessment ('FSA') package.
Maintained by Derek Ogle. Last updated 2 years ago.
fishfisheriesfisheries-stock-assessmentfishr-websitestock-assessment
33.5 match 13 stars 5.75 score 285 scripts
kbroman
qtl:Tools for Analyzing QTL Experiments
Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits. Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.
Maintained by Karl W Broman. Last updated 7 months ago.
14.7 match 80 stars 12.79 score 2.4k scripts 29 dependents
biodiverse
spAbundance:Univariate and Multivariate Spatial Modeling of Species Abundance
Fits single-species (univariate) and multi-species (multivariate) non-spatial and spatial abundance models in a Bayesian framework using Markov Chain Monte Carlo (MCMC). Spatial models are fit using Nearest Neighbor Gaussian Processes (NNGPs). Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2022) <doi:10.18637/jss.v103.i05>. Fits single-species and multi-species spatial and non-spatial versions of generalized linear mixed models (Gaussian, Poisson, Negative Binomial), N-mixture models (Royle 2004 <doi:10.1111/j.0006-341X.2004.00142.x>) and hierarchical distance sampling models (Royle, Dawson, Bates (2004) <doi:10.1890/03-3127>). Multi-species spatial models are fit using a spatial factor modeling approach with NNGPs for computational efficiency.
Maintained by Jeffrey Doser. Last updated 17 days ago.
28.3 match 17 stars 6.15 score 43 scripts 1 dependentsmazamascience
MazamaSpatialUtils:Spatial Data Download and Utility Functions
A suite of conversion functions to create internally standardized spatial polygons data frames. Utility functions use these data sets to return values such as country, state, time zone, watershed, etc. associated with a set of longitude/latitude pairs. (They also make cool maps.)
Maintained by Jonathan Callahan. Last updated 5 months ago.
21.5 match 5 stars 8.09 score 282 scripts 2 dependents
mrc-ide
orderly2:Orderly Next Generation
Distributed reproducible computing framework, adopting ideas from git, docker and other software. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.
Maintained by Rich FitzJohn. Last updated 2 months ago.
20.8 match 8 stars 8.30 score 49 scripts 2 dependents
cran
mgcv:Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) <doi:10.1201/9781315370279> for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.
Maintained by Simon Wood. Last updated 1 years ago.
12.4 match 32 stars 12.71 score 17k scripts 7.8k dependents
didiermurillof
FielDHub:A Shiny App for Design of Experiments in Life Sciences
A shiny design of experiments (DOE) app that aids in the creation of traditional, un-replicated, augmented and partially-replicated designs applied to agriculture, plant breeding, forestry, animal and biological sciences.
Maintained by Didier Murillo. Last updated 8 months ago.
agriculturalbreedingdesigndoeexperimentalplantbreedingshiny
17.3 match 48 stars 9.10 score 70 scripts 1 dependents
tidyverse
stringr:Simple, Consistent Wrappers for Common String Operations
A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.
Maintained by Hadley Wickham. Last updated 7 months ago.
6.2 match 622 stars 21.97 score 164k scripts 8.2k dependents
tarnduong
ks:Kernel Smoothing
Kernel smoothers for univariate and multivariate data, with comprehensive visualisation and bandwidth selection capabilities, including for densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.
Maintained by Tarn Duong. Last updated 6 months ago.
12.8 match 6 stars 10.14 score 920 scripts 262 dependents
ocean-tracking-network
glatos:A package for the Great Lakes Acoustic Telemetry Observation System
Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.
Maintained by Christopher Holbrook. Last updated 6 months ago.
20.1 match 10 stars 6.38 score 112 scripts
r-forge
robustbase:Basic Robust Statistics
"Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Maintained by Martin Maechler. Last updated 4 months ago.
8.7 match 13.33 score 1.7k scripts 480 dependents
bioc
biomaRt:Interface to BioMart databases (i.e. Ensembl)
In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (<http://www.biomart.org>). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.
Maintained by Mike Smith. Last updated 2 days ago.
annotationbioconductorbiomartensembl
7.1 match 38 stars 15.99 score 13k scripts 230 dependents
ropensci
rnoaa:'NOAA' Weather Data from R
Client for many 'NOAA' data sources including the 'NCDC' climate 'API' at <https://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for each of the 'API' 'endpoints': data, data categories, data sets, data types, locations, location categories, and stations. In addition, we have an interface for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS', tornado data via the 'NOAA' storm prediction center, and more.
Maintained by Daniel Hocking. Last updated 1 months ago.
earthscienceclimateprecipitationtemperaturestormbuoyncdcnoaatornadoesea iceisdnoaa-data
11.6 match 334 stars 9.39 score 788 scripts 4 dependents
paulojus
geoR:Analysis of Geostatistical Data
Geostatistical analysis including variogram-based, likelihood-based and Bayesian methods. Software companion for Diggle and Ribeiro (2007) <doi:10.1007/978-0-387-48536-2>.
Maintained by Paulo Justiniano Ribeiro Jr. Last updated 1 years ago.
14.1 match 10 stars 7.57 score 1.8k scripts 12 dependents
r-lib
desc:Manipulate DESCRIPTION Files
Tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.
Maintained by Gรกbor Csรกrdi. Last updated 1 months ago.
7.2 match 123 stars 14.68 score 409 scripts 1.1k dependents
inbo
watina:Querying and Processing Data from the INBO Watina Database
The R-package watina contains functions to query and process data from the Watina database at the Research Institute for Nature and Forest (INBO). This database primarily provides groundwater level and chemical data, mainly from natural areas in Flanders (Belgium).
Maintained by Floris Vanderhaeghe. Last updated 4 months ago.
groundwaterpreprocessing-functionsreproducibility
25.3 match 2 stars 4.16 score 24 scripts
jmsigner
amt:Animal Movement Tools
Manage and analyze animal movement data. The functionality of 'amt' includes methods to calculate home ranges, track statistics (e.g. step lengths, speed, or turning angles), prepare data for fitting habitat selection analyses, and simulation of space-use from fitted step-selection functions.
Maintained by Johannes Signer. Last updated 4 months ago.
9.7 match 41 stars 10.54 score 418 scripts
tbep-tech
tbeptools:Data and Indicators for the Tampa Bay Estuary Program
Several functions are provided for working with Tampa Bay Estuary Program data and indicators, including the water quality report card, tidal creek assessments, Tampa Bay Nekton Index, Tampa Bay Benthic Index, seagrass transect data, habitat report card, and fecal indicator bacteria. Additional functions are provided for miscellaneous tasks, such as reference library curation.
Maintained by Marcus Beck. Last updated 9 days ago.
data-analysistampa-baytbepwater-quality
12.9 match 10 stars 7.86 score 133 scriptsropensci
redland:RDF Library Bindings in R
Provides methods to parse, query and serialize information stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>. This package supports RDF by implementing an R interface to the Redland RDF C library, described at <https://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph consisting of Statements composed of Subject, Predicate, and Object Nodes.
Maintained by Matthew B. Jones. Last updated 1 years ago.
12.7 match 17 stars 7.85 score 98 scripts 13 dependents
womeimingzi11
amapGeocode:An Interface to the 'AutoNavi Maps' API Geocoding Services
Getting and parsing data of location geocode/reverse-geocode and administrative regions from 'AutoNavi Maps'<https://lbs.amap.com/api/webservice/summary> API.
Maintained by Han Chen. Last updated 1 years ago.
autonavigeocodegeocode-chinageocode-r
19.1 match 13 stars 5.04 score 17 scripts
jaseziv
worldfootballR:Extract and Clean World Football (Soccer) Data
Allow users to obtain clean and tidy football (soccer) game, team and player data. Data is collected from a number of popular sites, including 'FBref', transfer and valuations data from 'Transfermarkt'<https://www.transfermarkt.com/> and shooting location and other match stats data from 'Understat'<https://understat.com/>. It gives users the ability to access data more efficiently, rather than having to export data tables to files before being able to complete their analysis.
Maintained by Jason Zivkovic. Last updated 1 months ago.
fbreffootballfootball-datasoccer-datasports-datatransfermarktunderstat
9.4 match 506 stars 9.89 score 516 scripts 2 dependents
malaria-atlas-project
malariaAtlas:An R Interface to Open-Access Malaria Data, Hosted by the 'Malaria Atlas Project'
A suite of tools to allow you to download all publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from the 'Malaria Atlas Project' <https://malariaatlas.org/> servers as well as utility functions for plotting the downloaded data.
Maintained by Mauricio van den Berg. Last updated 8 months ago.
10.2 match 44 stars 9.10 score 118 scripts 3 dependentsbart1
move2:Processing and Analysing Animal Trajectories
Tools to handle, manipulate and explore trajectory data, with an emphasis on data from tracked animals. The package is designed to support large studies with several million location records and keep track of units where possible. Data import directly from 'movebank' <https://www.movebank.org/cms/movebank-main> and files is facilitated.
Maintained by Bart Kranstauber. Last updated 1 months ago.
12.2 match 7.51 score 169 scripts 1 dependents
msalibian
RobStatTM:Robust Statistics: Theory and Methods
Companion package for the book: "Robust Statistics: Theory and Methods, second edition", <http://www.wiley.com/go/maronna/robust>. This package contains code that implements the robust estimators discussed in the recent second edition of the book above, as well as the scripts reproducing all the examples in the book.
Maintained by Matias Salibian-Barrera. Last updated 3 days ago.
robustrobust-estimationrobust-regressionrobust-statisticsrobustnessstatisticsfortranopenblas
8.8 match 17 stars 10.23 score 84 scripts 8 dependents
evolecolgroup
pastclim:Manipulate Time Series of Climate Reconstructions
Methods to easily extract and manipulate climate reconstructions for ecological and anthropological analyses, as described in Leonardi et al. (2023) <doi:10.1111/ecog.06481>. The package includes datasets of palaeoclimate reconstructions, present observations, and future projections from multiple climate models.
Maintained by Andrea Manica. Last updated 3 days ago.
climate-datapaleoclimatespecies-distribution-modelling
11.1 match 38 stars 8.12 score 49 scripts
rqtl
qtl2:Quantitative Trait Locus Mapping in Experimental Crosses
Provides a set of tools to perform quantitative trait locus (QTL) analysis in experimental crosses. It is a reimplementation of the 'R/qtl' package to better handle high-dimensional data and complex cross designs. Broman et al. (2019) <doi:10.1534/genetics.118.301595>.
Maintained by Karl W Broman. Last updated 8 days ago.
9.4 match 34 stars 9.48 score 1.1k scripts 5 dependentsropensci
stplanr:Sustainable Transport Planning
Tools for transport planning with an emphasis on spatial transport data and non-motorized modes. The package was originally developed to support the 'Propensity to Cycle Tool', a publicly available strategic cycle network planning tool (Lovelace et al. 2017) <doi:10.5198/jtlu.2016.862>, but has since been extended to support public transport routing and accessibility analysis (Moreno-Monroy et al. 2017) <doi:10.1016/j.jtrangeo.2017.08.012> and routing with locally hosted routing engines such as 'OSRM' (Lowans et al. 2023) <doi:10.1016/j.enconman.2023.117337>. The main functions are for creating and manipulating geographic "desire lines" from origin-destination (OD) data (building on the 'od' package); calculating routes on the transport network locally and via interfaces to routing services such as <https://cyclestreets.net/> (Desjardins et al. 2021) <doi:10.1007/s11116-021-10197-1>; and calculating route segment attributes such as bearing. The package implements the 'travel flow aggregration' method described in Morgan and Lovelace (2020) <doi:10.1177/2399808320942779> and the 'OD jittering' method described in Lovelace et al. (2022) <doi:10.32866/001c.33873>. Further information on the package's aim and scope can be found in the vignettes and in a paper in the R Journal (Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053>, and in a paper outlining the landscape of open source software for geographic methods in transport planning (Lovelace, 2021) <doi:10.1007/s10109-020-00342-2>.
Maintained by Robin Lovelace. Last updated 7 months ago.
cyclecyclingdesire-linesorigin-destinationpeer-reviewedpubic-transportroute-networkroutesroutingspatialtransporttransport-planningtransportationwalking
7.1 match 427 stars 12.31 score 684 scripts 3 dependents
ironholds
olctools:Open Location Code Handling in R
'Open Location Codes' (https://openlocationcode.com/) are a Google- created standard for identifying geographic locations. olctools provides utilities for validating, encoding and decoding entries that follow this standard.
Maintained by Oliver Keyes. Last updated 9 years ago.
16.9 match 13 stars 5.16 score 11 scripts
eldarrak
FLightR:Reconstruct Animal Paths from Solar Geolocation Loggers Data
Spatio-temporal locations of an animal are computed from annotated data with a hidden Markov model via particle filter algorithm. The package is relatively robust to varying degrees of shading. The hidden Markov model is described in Movement Ecology - Rakhimberdiev et al. (2015) <doi:10.1186/s40462-015-0062-5>, general package description is in the Methods in Ecology and Evolution - Rakhimberdiev et al. (2017) <doi:10.1111/2041-210X.12765> and package accuracy assessed in the Journal of Avian Biology - Rakhimberdiev et al. (2016) <doi:10.1111/jav.00891>.
Maintained by Eldar Rakhimberdiev. Last updated 6 months ago.
movement-ecologysolar-geolocation-loggerssolar-geolocator
11.9 match 22 stars 7.26 score 111 scripts
elipousson
getdata:Get Easy Access to Tabular and Spatial Data
Download and format spatial and non-spatial data with simple filtering by location.
Maintained by Eli Pousson. Last updated 5 months ago.
19.3 match 12 stars 4.46 score 18 scripts 3 dependents
r-spatial
stars:Spatiotemporal Arrays, Raster and Vector Data Cubes
Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Maintained by Edzer Pebesma. Last updated 30 days ago.
4.7 match 571 stars 18.27 score 7.2k scripts 137 dependents
dsjohnson
crawl:Fit Continuous-Time Correlated Random Walk Models to Animal Movement Data
Fit continuous-time correlated random walk models with time indexed covariates to animal telemetry data. The model is fit using the Kalman-filter on a state space version of the continuous-time stochastic movement process.
Maintained by Devin S. Johnson. Last updated 5 months ago.
13.7 match 19 stars 6.29 score 63 scripts 3 dependents
lindbrook
cholera:Amend, Augment and Aid Analysis of John Snow's Cholera Map
Amends errors, augments data and aids analysis of John Snow's map of the 1854 London cholera outbreak.
Maintained by lindbrook. Last updated 1 days ago.
choleradata-visualizationdatasetsepidemiologyjohn-snowpublic-healthtriangulation-delaunayvoronoivoronoi-polygons
9.1 match 136 stars 9.33 score 95 scripts
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.
4.6 match 127 stars 18.63 score 35k scripts 1.3k dependentsvalentint
rrcovNA:Scalable Robust Estimators with High Breakdown Point for Incomplete Data
Robust Location and Scatter Estimation and Robust Multivariate Analysis with High Breakdown Point for Incomplete Data (missing values) (Todorov et al. (2010) <doi:10.1007/s11634-010-0075-2>).
Maintained by Valentin Todorov. Last updated 3 months ago.
22.4 match 1 stars 3.77 score 59 scriptsbioc
CARDspa:Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics
CARD is a reference-based deconvolution method that estimates cell type composition in spatial transcriptomics based on cell type specific expression information obtained from a reference scRNA-seq data. A key feature of CARD is its ability to accommodate spatial correlation in the cell type composition across tissue locations, enabling accurate and spatially informed cell type deconvolution as well as refined spatial map construction. CARD relies on an efficient optimization algorithm for constrained maximum likelihood estimation and is scalable to spatial transcriptomics with tens of thousands of spatial locations and tens of thousands of genes.
Maintained by Jing Fu. Last updated 16 days ago.
spatialsinglecelltranscriptomicsvisualizationopenblascppopenmp
18.6 match 4.54 score 3 scriptsbioc
rhdf5:R Interface to HDF5
This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.
Maintained by Mike Smith. Last updated 2 months ago.
infrastructuredataimporthdf5rhdf5opensslcurlzlibcpp
5.3 match 62 stars 15.93 score 4.2k scripts 232 dependents
asgr
imager:Image Processing Library Based on 'CImg'
Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.
Maintained by Aaron Robotham. Last updated 27 days ago.
6.1 match 17 stars 13.62 score 2.4k scripts 45 dependentsr-forge
distrMod:Object Oriented Implementation of Probability Models
Implements S4 classes for probability models based on packages 'distr' and 'distrEx'.
Maintained by Peter Ruckdeschel. Last updated 2 months ago.
12.2 match 6.71 score 139 scripts 6 dependentsr-lib
testthat:Unit Testing for R
Software testing is important, but, in part because it is frustrating and boring, many of us avoid it. 'testthat' is a testing framework for R that is easy to learn and use, and integrates with your existing 'workflow'.
Maintained by Hadley Wickham. Last updated 16 days ago.
3.9 match 900 stars 20.97 score 74k scripts 465 dependents
mandymejia
ciftiTools:Tools for Reading, Writing, Viewing and Manipulating CIFTI Files
CIFTI files contain brain imaging data in "grayordinates," which represent the gray matter as cortical surface vertices (left and right) and subcortical voxels (cerebellum, basal ganglia, and other deep gray matter). 'ciftiTools' provides a unified environment for reading, writing, visualizing and manipulating CIFTI-format data. It supports the "dscalar," "dlabel," and "dtseries" intents. Grayordinate data is read in as a "xifti" object, which is structured for convenient access to the data and metadata, and includes support for surface geometry files to enable spatially-dependent functionality such as static or interactive visualizations and smoothing.
Maintained by Amanda Mejia. Last updated 2 months ago.
9.1 match 47 stars 8.90 score 176 scripts 4 dependents
ianjonsen
aniMotum:Fit Continuous-Time State-Space and Latent Variable Models for Quality Control of Argos Satellite (and Other) Telemetry Data and for Estimating Changes in Animal Movement
Fits continuous-time random walk, correlated random walk and move persistence state-space models for location estimation and behavioural inference from animal tracking data ('Argos', processed light-level 'geolocation', 'GPS'). Template Model Builder ('TMB') is used for fast random-effects estimation. The 'Argos' data can be: (older) least squares-based locations; (newer) Kalman filter-based locations with error ellipse information; or a mixture of both. The models estimate two sets of location states corresponding to: 1) each observation, which are (usually) irregularly timed; and 2) user-specified time intervals (regular or irregular). A track re-routing function is provided to adjust location estimates for known movement barriers. Track simulation functions are provided. Latent variable models are also provided to estimate move persistence from track data not requiring state-space model filtering.
Maintained by Ian Jonsen. Last updated 10 days ago.
animal-movementanimal-trackingrandom-effects-modelstate-space-modelstmbcpp
11.2 match 39 stars 7.16 score 59 scripts
paballand
EconGeo:Computing Key Indicators of the Spatial Distribution of Economic Activities
Functions to compute a series of indices commonly used in the fields of economic geography, economic complexity, and evolutionary economics to describe the location, distribution, spatial organization, structure, and complexity of economic activities. Functions include basic spatial indicators such as the location quotient, the Krugman specialization index, the Herfindahl or the Shannon entropy indices but also more advanced functions to compute different forms of normalized relatedness between economic activities or network-based measures of economic complexity. Most of the functions use matrix calculus and are based on bipartite (incidence) matrices consisting of region - industry pairs.
Maintained by Pierre-Alexandre Balland. Last updated 2 years ago.
16.1 match 41 stars 4.96 score 44 scriptsbioc
marray:Exploratory analysis for two-color spotted microarray data
Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.
Maintained by Yee Hwa (Jean) Yang. Last updated 5 months ago.
microarraytwochannelpreprocessing
9.0 match 8.92 score 222 scripts 37 dependents
bnosac
udpipe:Tokenization, Parts of Speech Tagging, Lemmatization and Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
This natural language processing toolkit provides language-agnostic 'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency parsing' of raw text. Next to text parsing, the package also allows you to train annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided at <https://universaldependencies.org/format.html>. The techniques are explained in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0 with UDPipe', available at <doi:10.18653/v1/K17-3009>. The toolkit also contains functionalities for commonly used data manipulations on texts which are enriched with the output of the parser. Namely functionalities and algorithms for collocations, token co-occurrence, document term matrix handling, term frequency inverse document frequency calculations, information retrieval metrics (Okapi BM25), handling of multi-word expressions, keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntactical patterns) sentiment scoring and semantic similarity analysis.
Maintained by Jan Wijffels. Last updated 2 years ago.
conlldependency-parserlemmatizationnatural-language-processingnlppos-taggingr-pkgrcpptext-miningtokenizerudpipecpp
6.7 match 215 stars 11.83 score 1.2k scripts 9 dependents
bczernecki
climate:Interface to Download Meteorological (and Hydrological) Datasets
Automatize downloading of meteorological and hydrological data from publicly available repositories: OGIMET (<http://ogimet.com/index.phtml.en>), University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair/>), Polish Institute of Meteorology and Water Management - National Research Institute (<https://danepubliczne.imgw.pl>), and National Oceanic & Atmospheric Administration (NOAA). This package also allows for searching geographical coordinates for each observation and calculate distances to the nearest stations.
Maintained by Bartosz Czernecki. Last updated 10 days ago.
climateclimate-dataimgwmeteorological-datameteorologynoaa-dataogimetsounding
10.3 match 88 stars 7.61 score 38 scripts
gamlss-dev
gamlss:Generalized Additive Models for Location Scale and Shape
Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.
Maintained by Mikis Stasinopoulos. Last updated 4 months ago.
6.9 match 16 stars 11.23 score 2.0k scripts 49 dependentsbioc
GenomicFeatures:Query the gene models of a given organism/assembly
Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.
Maintained by H. Pagรจs. Last updated 4 months ago.
geneticsinfrastructureannotationsequencinggenomeannotationbioconductor-packagecore-package
5.1 match 26 stars 15.34 score 5.3k scripts 339 dependents
usaid-oha-si
gisr:Geospatial Analytics Utility functions
R Spatial functions for HIV/AIDS related Geospatial Analytics.
Maintained by Baboyma Kagniniwa. Last updated 1 years ago.
14.5 match 2 stars 5.29 score 328 scriptsbioc
annotate:Annotation for microarrays
Using R enviroments for annotation.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
6.7 match 11.41 score 812 scripts 243 dependents
great-northern-diver
loon:Interactive Statistical Data Visualization
An extendable toolkit for interactive data visualization and exploration.
Maintained by R. Wayne Oldford. Last updated 2 years ago.
data-analysisdata-sciencedata-visualizationexploratory-analysisexploratory-data-analysishigh-dimensional-datainteractive-graphicsinteractive-visualizationsloonpythonstatistical-analysisstatistical-graphicsstatisticstcl-extensiontk
8.2 match 48 stars 9.00 score 93 scripts 5 dependentstidyverse
dplyr:A Grammar of Data Manipulation
A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
Maintained by Hadley Wickham. Last updated 13 days ago.
3.0 match 4.8k stars 24.68 score 659k scripts 7.8k dependents
gagolews
stringi:Fast and Portable Character String Processing Facilities
A collection of character string/text/natural language processing tools for pattern searching (e.g., with 'Java'-like regular expressions or the 'Unicode' collation algorithm), random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date-time formatting and parsing, and many more. They are fast, consistent, convenient, and - thanks to 'ICU' (International Components for Unicode) - portable across all locales and platforms. Documentation about 'stringi' is provided via its website at <https://stringi.gagolewski.com/> and the paper by Gagolewski (2022, <doi:10.18637/jss.v103.i02>).
Maintained by Marek Gagolewski. Last updated 1 months ago.
icuicu4cnatural-language-processingnlpregexregexpstring-manipulationstringistringrtexttext-processingtidy-dataunicodecpp
4.0 match 309 stars 18.31 score 10k scripts 8.6k dependents
julianfaraway
faraway:Datasets and Functions for Books by Julian Faraway
Books are "Linear Models with R" published 1st Ed. August 2004, 2nd Ed. July 2014, 3rd Ed. February 2025 by CRC press, ISBN 9781439887332, and "Extending the Linear Model with R" published by CRC press in 1st Ed. December 2005 and 2nd Ed. March 2016, ISBN 9781584884248 and "Practical Regression and ANOVA in R" contributed documentation on CRAN (now very dated).
Maintained by Julian Faraway. Last updated 1 months ago.
7.5 match 29 stars 9.43 score 1.7k scripts 1 dependentsr-lib
here:A Simpler Way to Find Your Files
Constructs paths to your project's files. Declare the relative path of a file within your project with 'i_am()'. Use the 'here()' function as a drop-in replacement for 'file.path()', it will always locate the files relative to your project root.
Maintained by Kirill Mรผller. Last updated 12 hours ago.
3.6 match 417 stars 19.62 score 96k scripts 607 dependentsr-forge
distr:Object Oriented Implementation of Distributions
S4-classes and methods for distributions.
Maintained by Peter Ruckdeschel. Last updated 2 months ago.
7.8 match 8.84 score 327 scripts 32 dependents
joshuaulrich
xts:eXtensible Time Series
Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.
Maintained by Joshua M. Ulrich. Last updated 4 months ago.
3.8 match 221 stars 18.38 score 12k scripts 654 dependents
vegandevs
vegan:Community Ecology Package
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Maintained by Jari Oksanen. Last updated 16 days ago.
ecological-modellingecologyordinationfortranopenblas
3.5 match 472 stars 19.41 score 15k scripts 440 dependents
reconhub
epiflows:Predicting Disease Spread from Flow Data
Provides functions and classes designed to handle and visualise epidemiological flows between locations. Also contains a statistical method for predicting disease spread from flow data initially described in Dorigatti et al. (2017) <doi:10.2807/1560-7917.ES.2017.22.28.30572>. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Maintained by Pawel Piatkowski. Last updated 1 years ago.
10.9 match 18 stars 6.16 score 20 scripts
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 19 days ago.
aspectdistancefragmentationfragmentation-indicesgisgrassgrass-gisrasterraster-projectionrasterizeslopetopographyvectorization
8.7 match 58 stars 7.69 score 8 scripts
njtierney
maxcovr:A Set of Tools For Solving The Maximal Covering Location Problem
Solving the "maximal covering location problem" as described by Church can be difficult for users not familiar with linear programming. maxcovr provides functions to make it easy to solve this problem, and tools to calculate facility coverage.
Maintained by Nicholas Tierney. Last updated 4 months ago.
11.1 match 44 stars 6.06 score 43 scripts
gianmarcoalberti
movecost:Calculation of Slope-Dependant Accumulated Cost Surface, Least-Cost Paths, Least-Cost Corridors, Least-Cost Networks Related to Human Movement Across the Landscape
Provides the facility to calculate non-isotropic accumulated cost surface, least-cost paths, least-cost corridors, least-cost networks using a number of human-movement-related cost functions that can be selected by the user. It just requires a Digital Terrain Model, a start location and (optionally) destination locations. See Alberti (2019) <doi:10.1016/j.softx.2019.100331>.
Maintained by Gianmarco Alberti. Last updated 1 years ago.
23.2 match 3 stars 2.86 score 48 scripts
spluque
diveMove:Dive Analysis and Calibration
Utilities to represent, visualize, filter, analyse, and summarize time-depth recorder (TDR) data. Miscellaneous functions for handling location data are also provided.
Maintained by Sebastian P. Luque. Last updated 5 months ago.
animal-behaviorbehavioural-ecologybiologydivingscience
9.6 match 6 stars 6.75 score 55 scripts
quanteda
quanteda:Quantitative Analysis of Textual Data
A fast, flexible, and comprehensive framework for quantitative text analysis in R. Provides functionality for corpus management, creating and manipulating tokens and n-grams, exploring keywords in context, forming and manipulating sparse matrices of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and distances, applying content dictionaries, applying supervised and unsupervised machine learning, visually representing text and text analyses, and more.
Maintained by Kenneth Benoit. Last updated 2 months ago.
corpusnatural-language-processingquantedatext-analyticsonetbbcpp
3.9 match 851 stars 16.68 score 5.4k scripts 51 dependents
f-silva-archaeo
skyscapeR:Data Analysis and Visualization for Skyscape Archaeology
Data reduction, visualization and statistical analysis of measurements of orientation of archaeological structures, following Silva (2020) <doi:10.1016/j.jas.2020.105138>.
Maintained by Silva Fabio. Last updated 6 months ago.
12.1 match 5 stars 5.31 score 41 scripts
pet221
SSNbler:Assemble 'SSN' Objects
Import, create and assemble data needed to fit spatial-statistical stream-network models using the 'SSN2' package for 'R'. Streams, observations, and prediction locations are represented as simple features and specific tools provided to define topological relationships between features; calculate the hydrologic distances (with flow-direction preserved) and the spatial additive function used to weight converging stream segments; and export the topological, spatial, and attribute information to an `SSN` (spatial stream network) object, which can be efficiently stored, accessed and analysed in 'R'. A detailed description of methods used to calculate and format the spatial data can be found in Peterson, E.E. and Ver Hoef, J.M., (2014) <doi:10.18637/jss.v056.i02>.
Maintained by Erin Peterson. Last updated 6 months ago.
10.4 match 10 stars 6.01 score 17 scripts
umr-amap
StormR:Analyzing the Behaviour of Wind Generated by Tropical Storms and Cyclones
Set of functions to quantify and map the behaviour of winds generated by tropical storms and cyclones in space and time. It includes functions to compute and analyze fields such as the maximum sustained wind field, power dissipation index and duration of exposure to winds above a given threshold. It also includes functions to map the trajectories as well as characteristics of the storms.
Maintained by Thomas Arsouze. Last updated 3 months ago.
cyclones-behaviourtropical-storms
8.4 match 14 stars 7.36 score 7 scriptsropensci
excluder:Checks for Exclusion Criteria in Online Data
Data that are collected through online sources such as Mechanical Turk may require excluding rows because of IP address duplication, geolocation, or completion duration. This package facilitates exclusion of these data for Qualtrics datasets.
Maintained by Jeffrey R. Stevens. Last updated 11 days ago.
datacleaningexclusionmturkqualtrics
11.0 match 9 stars 5.51 score 18 scriptsrstudio
tfprobability:Interface to 'TensorFlow Probability'
Interface to 'TensorFlow Probability', a 'Python' library built on 'TensorFlow' that makes it easy to combine probabilistic models and deep learning on modern hardware ('TPU', 'GPU'). 'TensorFlow Probability' includes a wide selection of probability distributions and bijectors, probabilistic layers, variational inference, Markov chain Monte Carlo, and optimizers such as Nelder-Mead, BFGS, and SGLD.
Maintained by Tomasz Kalinowski. Last updated 3 years ago.
7.0 match 54 stars 8.63 score 221 scripts 3 dependents
davidasmith
whatthreewords:Work with the 'what3words' API for Easy Location Referencing
Use the 'what3words' API <https://developer.what3words.com/public-api> to return three words which uniquely identify every 3m x 3m square on Earth. It is also possible to return coordinates from any valid three words location. Supports multiple languages.
Maintained by David Smith. Last updated 1 years ago.
geocodinggeolocationlocationwhat3wordswhat3words-api
16.2 match 3.70 score 6 scriptsropensci
geonames:Interface to the "Geonames" Spatial Query Web Service
The web service at <https://www.geonames.org/> provides a number of spatial data queries, including administrative area hierarchies, city locations and some country postal code queries. A (free) username is required and rate limits exist.
Maintained by Barry Rowlingson. Last updated 6 years ago.
7.0 match 37 stars 8.45 score 165 scripts 21 dependentsbioc
gwascat:representing and modeling data in the EMBL-EBI GWAS catalog
Represent and model data in the EMBL-EBI GWAS catalog.
Maintained by VJ Carey. Last updated 5 months ago.
9.8 match 6.05 score 110 scripts 2 dependents
dankelley
oce:Analysis of Oceanographic Data
Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively by Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.
Maintained by Dan Kelley. Last updated 1 days ago.
3.8 match 146 stars 15.42 score 4.2k scripts 18 dependents
tidymodels
butcher:Model Butcher
Provides a set of S3 generics to axe components of fitted model objects and help reduce the size of model objects saved to disk.
Maintained by Julia Silge. Last updated 13 days ago.
5.0 match 132 stars 11.54 score 146 scripts 13 dependents
tianxia-jia
mcgf:Markov Chain Gaussian Fields Simulation and Parameter Estimation
Simulating and estimating (regime-switching) Markov chain Gaussian fields with covariance functions of the Gneiting class (Gneiting 2002) <doi:10.1198/016214502760047113>. It supports parameter estimation by weighted least squares and maximum likelihood methods, and produces Kriging forecasts and intervals for existing and new locations.
Maintained by Tianxia Jia. Last updated 9 months ago.
12.0 match 1 stars 4.82 score 11 scriptsropensci
rebird:R Client for the eBird Database of Bird Observations
A programmatic client for the eBird database (<https://ebird.org/home>), including functions for searching for bird observations by geographic location (latitude, longitude), eBird hotspots, location identifiers, by notable sightings, by region, and by taxonomic name.
Maintained by Sebastian Pardo. Last updated 1 months ago.
birdsbirdingebirddatabasedatabiologyobservationssightingsornithologyebird-apiebird-webservicesspocc
5.5 match 90 stars 10.43 score 73 scripts 6 dependents
ropengov
giscoR:Download Map Data from GISCO API - Eurostat
Tools to download data from the GISCO (Geographic Information System of the Commission) Eurostat database <https://ec.europa.eu/eurostat/web/gisco>. Global and European map data available. This package is in no way officially related to or endorsed by Eurostat.
Maintained by Diego Hernangรณmez. Last updated 30 days ago.
ropengovspatialapi-wrappereurostatgiscothematic-mapseurostat-dataggplot2gis
5.3 match 75 stars 10.70 score 424 scripts 5 dependents
davisvaughan
ivs:Interval Vectors
Provides a library for generic interval manipulations using a new interval vector class. Capabilities include: locating various kinds of relationships between two interval vectors, merging overlaps within a single interval vector, splitting an interval vector on its overlapping endpoints, and applying set theoretical operations on interval vectors. Many of the operations in this package were inspired by James Allen's interval algebra, Allen (1983) <doi:10.1145/182.358434>.
Maintained by Davis Vaughan. Last updated 2 years ago.
8.1 match 48 stars 7.05 score 39 scripts 2 dependentsbioc
coMethDMR:Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies
coMethDMR identifies genomic regions associated with continuous phenotypes by optimally leverages covariations among CpGs within predefined genomic regions. Instead of testing all CpGs within a genomic region, coMethDMR carries out an additional step that selects co-methylated sub-regions first without using any outcome information. Next, coMethDMR tests association between methylation within the sub-region and continuous phenotype using a random coefficient mixed effects model, which models both variations between CpG sites within the region and differential methylation simultaneously.
Maintained by Fernanda Veitzman. Last updated 5 months ago.
dnamethylationepigeneticsmethylationarraydifferentialmethylationgenomewideassociation
8.8 match 7 stars 6.47 score 42 scripts
usepa
spmodel:Spatial Statistical Modeling and Prediction
Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
Maintained by Michael Dumelle. Last updated 4 days ago.
7.4 match 15 stars 7.66 score 112 scripts 3 dependents
zzawadz
DepthProc:Statistical Depth Functions for Multivariate Analysis
Data depth concept offers a variety of powerful and user friendly tools for robust exploration and inference for multivariate data. The offered techniques may be successfully used in cases of lack of our knowledge on parametric models generating data due to their nature. The package consist of among others implementations of several data depth techniques involving multivariate quantile-quantile plots, multivariate scatter estimators, multivariate Wilcoxon tests and robust regressions.
Maintained by Zygmunt Zawadzki. Last updated 3 years ago.
depth-functionsexploratory-data-analysisstatisticsopenblascppopenmp
10.7 match 6 stars 5.27 score 104 scripts 2 dependentsbioc
BiocFileCache:Manage Files Across Sessions
This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.
Maintained by Lori Shepherd. Last updated 2 months ago.
dataimportcore-packageu24ca289073
4.0 match 13 stars 13.76 score 486 scripts 429 dependentscran
MASS:Support Functions and Datasets for Venables and Ripley's MASS
Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).
Maintained by Brian Ripley. Last updated 16 days ago.
5.3 match 19 stars 10.53 score 11k dependents
data-cleaning
errorlocate:Locate Errors with Validation Rules
Errors in data can be located and removed using validation rules from package 'validate'. See also Van der Loo and De Jonge (2018) <doi:10.1002/9781118897126>, chapter 7.
Maintained by Edwin de Jonge. Last updated 9 months ago.
data-cleaningerrorsinvalidation
9.0 match 22 stars 6.11 score 59 scripts
tsmodels
tsdistributions:Location Scale Standardized Distributions
Location-Scale based distributions parameterized in terms of mean, standard deviation, skew and shape parameters and estimation using automatic differentiation. Distributions include the Normal, Student and GED as well as their skewed variants ('Fernandez and Steel'), the 'Johnson SU', and the Generalized Hyperbolic. Also included is the semi-parametric piece wise distribution ('spd') with Pareto tails and kernel interior.
Maintained by Alexios Galanos. Last updated 4 months ago.
distributionsfinanceprobability-distributionprobability-distributionsstatistical-distributionstimeseriescpp
8.3 match 4 stars 6.66 score 19 scripts 2 dependentsbioc
rCGH:Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools. rCGH also supports custom arrays, provided data complies with the expected format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to profiles segmentation and gene annotations. This package also provides several visualization functions (static or interactive) which facilitate individual profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.
Maintained by Frederic Commo. Last updated 5 months ago.
acghcopynumbervariationpreprocessingfeatureextraction
10.8 match 4 stars 5.10 score 26 scripts 1 dependents
kenaho1
asbio:A Collection of Statistical Tools for Biologists
Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Maintained by Ken Aho. Last updated 2 months ago.
7.5 match 5 stars 7.32 score 310 scripts 3 dependents
mbtyers
riverdist:River Network Distance Computation and Applications
Reads river network shape files and computes network distances. Also included are a variety of computation and graphical tools designed for fisheries telemetry research, such as minimum home range, kernel density estimation, and clustering analysis using empirical k-functions with a bootstrap envelope. Tools are also provided for editing the river networks, meaning there is no reliance on external software.
Maintained by Matt Tyers. Last updated 4 months ago.
7.3 match 26 stars 7.50 score 96 scripts
traitecoevo
austraits:Helpful functions to access the AusTraits database and wrangle data from other traits.build databases
`austraits` allow users to **access, explore and wrangle data** from traits.build relational databases. It is also an R interface to AusTraits, the Australian plant trait database. This package contains functions for joining data from various tables, filtering to specific records, combining multiple databases and visualising the distribution of the data. We expect this package will assist users in working with `traits.build` databases.
Maintained by Fonti Kar. Last updated 2 months ago.
9.2 match 22 stars 5.93 score 43 scripts 1 dependents
andreyshabalin
MatrixEQTL:Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations
Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix eQTL can test for association between genotype and gene expression using linear regression with either additive or ANOVA genotype effects. The models can include covariates to account for factors as population stratification, gender, and clinical variables. It also supports models with heteroscedastic and/or correlated errors, false discovery rate estimation and separate treatment of local (cis) and distant (trans) eQTLs. For more details see Shabalin (2012) <doi:10.1093/bioinformatics/bts163>.
Maintained by Andrey A Shabalin. Last updated 1 years ago.
6.7 match 69 stars 8.10 score 612 scripts 2 dependents
frbcesab
funbiogeo:Functional Biogeography Analyses
Helps users with analyses in functional biogeogeography by loading and combining data, computing trait coverage, as well as computing functional diversity indices, drawing maps, correlating them with the environment, and upscaling assemblages.
Maintained by Nicolas Casajus. Last updated 4 days ago.
functional-biogeographyfunctional-diversityfunctional-trait
9.6 match 11 stars 5.60 score 8 scripts
geobosh
cvar:Compute Expected Shortfall and Value at Risk for Continuous Distributions
Compute expected shortfall (ES) and Value at Risk (VaR) from a quantile function, distribution function, random number generator or probability density function. ES is also known as Conditional Value at Risk (CVaR). Virtually any continuous distribution can be specified. The functions are vectorized over the arguments. The computations are done directly from the definitions, see e.g. Acerbi and Tasche (2002) <doi:10.1111/1468-0300.00091>. Some support for GARCH models is provided, as well.
Maintained by Georgi N. Boshnakov. Last updated 2 years ago.
expected-shortfalllocations-scale-transformationsquantilequantile-functionsriskvalue-at-risk
6.7 match 6 stars 8.05 score 27 scripts 52 dependents
alshum
rwunderground:R Interface to Weather Underground API
Tools for getting historical weather information and forecasts from wunderground.com. Historical weather and forecast data includes, but is not limited to, temperature, humidity, windchill, wind speed, dew point, heat index. Additionally, the weather underground weather API also includes information on sunrise/sunset, tidal conditions, satellite/webcam imagery, weather alerts, hurricane alerts and historical high/low temperatures.
Maintained by Eric Hare. Last updated 7 years ago.
weatherweather-dataweather-historyweather-underground
8.6 match 77 stars 6.20 score 83 scriptsgamlss-dev
gamlss.dist:Distributions for Generalized Additive Models for Location Scale and Shape
A set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape, Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a 'log' or a 'logit' transformation respectively.
Maintained by Mikis Stasinopoulos. Last updated 21 days ago.
5.1 match 4 stars 10.50 score 346 scripts 71 dependents
takahiroshimada
SDLfilter:Filtering and Assessing the Sample Size of Tracking Data
Functions to filter GPS/Argos locations, as well as assessing the sample size for the analysis of animal distributions. The filters remove temporal and spatial duplicates, fixes located at a given height from estimated high tide line, and locations with high error as described in Shimada et al. (2012) <doi:10.3354/meps09747> and Shimada et al. (2016) <doi:10.1007/s00227-015-2771-0>. Sample size for the analysis of animal distributions can be assessed by the conventional area-based approach or the alternative probability-based approach as described in Shimada et al. (2021) <doi:10.1111/2041-210X.13506>.
Maintained by Takahiro Shimada. Last updated 1 years ago.
14.1 match 7 stars 3.77 score 17 scripts
eborgnine
geostatsp:Geostatistical Modelling with Likelihood and Bayes
Geostatistical modelling facilities using 'SpatRaster' and 'SpatVector' objects are provided. Non-Gaussian models are fit using 'INLA', and Gaussian geostatistical models use Maximum Likelihood Estimation. For details see Brown (2015) <doi:10.18637/jss.v063.i12>. The 'RandomFields' package is available at <https://www.wim.uni-mannheim.de/schlather/publications/software>.
Maintained by Patrick Brown. Last updated 1 months ago.
13.5 match 5 stars 3.94 score 73 scriptselipousson
maplayer:Make Map Layers With ggplot2
Make map-making with ggplot2 and sf more convenient with layers that subset by location.
Maintained by Eli Pousson. Last updated 6 months ago.
16.3 match 9 stars 3.26 score 7 scripts
brry
berryFunctions:Function Collection Related to Plotting and Hydrology
Draw horizontal histograms, color scattered points by 3rd dimension, enhance date- and log-axis plots, zoom in X11 graphics, trace errors and warnings, use the unit hydrograph in a linear storage cascade, convert lists to data.frames and arrays, fit multiple functions.
Maintained by Berry Boessenkool. Last updated 1 months ago.
5.6 match 13 stars 9.43 score 350 scripts 16 dependents
mkln
meshed:Bayesian Regression with Meshed Gaussian Processes
Fits Bayesian regression models based on latent Meshed Gaussian Processes (MGP) as described in Peruzzi, Banerjee, Finley (2020) <doi:10.1080/01621459.2020.1833889>, Peruzzi, Banerjee, Dunson, and Finley (2021) <arXiv:2101.03579>, Peruzzi and Dunson (2024) <arXiv:2201.10080>. Funded by ERC grant 856506 and NIH grant R01ES028804.
Maintained by Michele Peruzzi. Last updated 7 months ago.
bayesianmcmcmultivariateregressionspatialspatiotemporalopenblascppopenmp
8.6 match 13 stars 6.11 score 49 scripts
inlabru-org
fmesher:Triangle Meshes and Related Geometry Tools
Generate planar and spherical triangle meshes, compute finite element calculations for 1- and 2-dimensional flat and curved manifolds with associated basis function spaces, methods for lines and polygons, and transparent handling of coordinate reference systems and coordinate transformation, including 'sf' and 'sp' geometries. The core 'fmesher' library code was originally part of the 'INLA' package, and implements parts of "Triangulations and Applications" by Hjelle and Daehlen (2006) <doi:10.1007/3-540-33261-8>.
Maintained by Finn Lindgren. Last updated 2 days ago.
4.7 match 16 stars 11.18 score 261 scripts 26 dependentsrstudio
renv:Project Environments
A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.
Maintained by Kevin Ushey. Last updated 3 days ago.
2.8 match 1.0k stars 18.55 score 1.5k scripts 113 dependentsbioc
RcisTarget:RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions
RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).
Maintained by Gert Hulselmans. Last updated 5 months ago.
generegulationmotifannotationtranscriptomicstranscriptiongenesetenrichmentgenetarget
5.5 match 37 stars 9.47 score 191 scripts
sevvandi
stxplore:Exploration of Spatio-Temporal Data
A set of statistical tools for spatio-temporal data exploration. Includes simple plotting functions, covariance calculations and computations similar to principal component analysis for spatio-temporal data. Can use both dataframes and stars objects for all plots and computations. For more details refer 'Spatio-Temporal Statistics with R' (Christopher K. Wikle, Andrew Zammit-Mangion, Noel Cressie, 2019, ISBN:9781138711136).
Maintained by Sevvandi Kandanaarachchi. Last updated 2 years ago.
11.1 match 5 stars 4.70 score 7 scripts
egpivo
SpatPCA:Regularized Principal Component Analysis for Spatial Data
Provide regularized principal component analysis incorporating smoothness, sparseness and orthogonality of eigen-functions by using the alternating direction method of multipliers algorithm (Wang and Huang, 2017, <DOI:10.1080/10618600.2016.1157483>). The method can be applied to either regularly or irregularly spaced data, including 1D, 2D, and 3D.
Maintained by Wen-Ting Wang. Last updated 7 months ago.
admmcovariance-estimationeigenfunctionslassomatrix-factorizationpcarcpparmadillorcppparallelregularizationspatialspatial-data-analysissplinesopenblascppopenmp
9.4 match 20 stars 5.53 score 17 scriptsropensci
geojsonio:Convert Data from and to 'GeoJSON' or 'TopoJSON'
Convert data to 'GeoJSON' or 'TopoJSON' from various R classes, including vectors, lists, data frames, shape files, and spatial classes. 'geojsonio' does not aim to replace packages like 'sp', 'rgdal', 'rgeos', but rather aims to be a high level client to simplify conversions of data from and to 'GeoJSON' and 'TopoJSON'.
Maintained by Michael Mahoney. Last updated 1 years ago.
geojsontopojsongeospatialconversiondatainput-outputio
4.8 match 151 stars 10.80 score 2.9k scripts 13 dependents
natverse
nat:NeuroAnatomy Toolbox for Analysis of 3D Image Data
NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Maintained by Gregory Jefferis. Last updated 5 months ago.
3dconnectomicsimage-analysisneuroanatomyneuroanatomy-toolboxneuronneuron-morphologyneurosciencevisualisation
5.2 match 67 stars 9.94 score 436 scripts 2 dependentsbioc
REMP:Repetitive Element Methylation Prediction
Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE.
Maintained by Yinan Zheng. Last updated 5 months ago.
dnamethylationmicroarraymethylationarraysequencinggenomewideassociationepigeneticspreprocessingmultichanneltwochanneldifferentialmethylationqualitycontroldataimport
8.7 match 2 stars 5.94 score 18 scriptscran
mix:Estimation/Multiple Imputation for Mixed Categorical and Continuous Data
Estimation/multiple imputation programs for mixed categorical and continuous data.
Maintained by Brian Ripley. Last updated 3 months ago.
12.1 match 2 stars 4.21 score 5 dependentsropensci
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 12 days ago.
gitgit-clientlibgit2libgit2-library
3.7 match 218 stars 13.86 score 836 scripts 49 dependents
gmbecker
switchr:Installing, Managing, and Switching Between Distinct Sets of Installed Packages
Provides an abstraction for managing, installing, and switching between sets of installed R packages. This allows users to maintain multiple package libraries simultaneously, e.g. to maintain strict, package-version-specific reproducibility of many analyses, or work within a development/production release paradigm. Introduces a generalized package installation process which supports multiple repository and non-repository sources and tracks package provenance.
Maintained by Gabriel Becker. Last updated 2 years ago.
7.8 match 59 stars 6.49 score 52 scripts
skranz
stringtools:Tools for working with strings in R
Tools for working with strings in R
Maintained by Sebastian Kranz. Last updated 3 years ago.
13.7 match 2 stars 3.66 score 29 scripts 26 dependents
luukvdmeer
sfnetworks:Tidy Geospatial Networks
Provides a tidy approach to spatial network analysis, in the form of classes and functions that enable a seamless interaction between the network analysis package 'tidygraph' and the spatial analysis package 'sf'.
Maintained by Lucas van der Meer. Last updated 3 months ago.
geospatial-networksnetwork-analysisrspatialsimple-featuresspatial-analysisspatial-data-sciencespatial-networkstidygraphtidyverse
5.2 match 372 stars 9.63 score 332 scripts 6 dependents
craddm
eegUtils:Utilities for Electroencephalographic (EEG) Analysis
Electroencephalography data processing and visualization tools. Includes import functions for 'BioSemi' (.BDF), 'Neuroscan' (.CNT), 'Brain Vision Analyzer' (.VHDR), 'EEGLAB' (.set) and 'Fieldtrip' (.mat). Many preprocessing functions such as referencing, epoching, filtering, and ICA are available. There are a variety of visualizations possible, including timecourse and topographical plotting.
Maintained by Matt Craddock. Last updated 5 months ago.
eegeeg-analysiseeg-dataeeg-signalseeg-signals-processingopenblascppopenmp
7.6 match 106 stars 6.54 score 82 scripts
rsheets
cellranger:Translate Spreadsheet Cell Ranges to Rows and Columns
Helper functions to work with spreadsheets and the "A1:D10" style of cell range specification.
Maintained by Jennifer Bryan. Last updated 7 years ago.
3.6 match 51 stars 13.84 score 80 scripts 843 dependents
mmm-uca
orloca:Operations Research LOCational Analysis Models
Objects and methods to handle and solve the min-sum location problem, also known as Fermat-Weber problem. The min-sum location problem search for a point such that the weighted sum of the distances to the demand points are minimized. See "The Fermat-Weber location problem revisited" by Brimberg, Mathematical Programming, 1, pg. 71-76, 1995. <DOI:10.1007/BF01592245>. General global optimization algorithms are used to solve the problem, along with the adhoc Weiszfeld method, see "Sur le point pour lequel la Somme des distances de n points donnes est minimum", by Weiszfeld, Tohoku Mathematical Journal, First Series, 43, pg. 355-386, 1937 or "On the point for which the sum of the distances to n given points is minimum", by E. Weiszfeld and F. Plastria, Annals of Operations Research, 167, pg. 7-41, 2009. <DOI:10.1007/s10479-008-0352-z>.
Maintained by Manuel Munoz-Marquez. Last updated 1 years ago.
13.7 match 3.64 score 24 scripts 2 dependentskbroman
xoi:Tools for Analyzing Crossover Interference
Analysis of crossover interference in experimental crosses, particularly regarding the gamma model. See, for example, Broman and Weber (2000) <doi:10.1086/302923>.
Maintained by Karl W Broman. Last updated 2 years ago.
13.1 match 4 stars 3.76 score 29 scriptsr-spatial
link2GI:Linking Geographic Information Systems, Remote Sensing and Other Command Line Tools
Functions and tools for using open GIS and remote sensing command-line interfaces in a reproducible environment.
Maintained by Chris Reudenbach. Last updated 4 months ago.
5.3 match 26 stars 9.05 score 78 scripts 1 dependentsropensci
EndoMineR:Functions to mine endoscopic and associated pathology datasets
This script comprises the functions that are used to clean up endoscopic reports and pathology reports as well as many of the scripts used for analysis. The scripts assume the endoscopy and histopathology data set is merged already but it can also be used of course with the unmerged datasets.
Maintained by Sebastian Zeki. Last updated 7 months ago.
endoscopygastroenterologypeer-reviewedsemi-structured-datatext-mining
8.9 match 13 stars 5.47 score 30 scripts
tomasfryda
h2o:R Interface for the 'H2O' Scalable Machine Learning Platform
R interface for 'H2O', the scalable open source machine learning platform that offers parallelized implementations of many supervised and unsupervised machine learning algorithms such as Generalized Linear Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests, Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes, Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, ModelSelection, Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).
Maintained by Tomas Fryda. Last updated 1 years ago.
5.9 match 3 stars 8.20 score 7.8k scripts 11 dependents
denironyx
overturemapsr:Download Overture Maps Data in R
Overture Maps offers free and open geospatial map data sourced from various providers and standardized to a common schema. This tool allows you to download Overture Maps data for a specific region of interest and convert it to several different file formats. For more information, visit <https://overturemaps.org/download/>.
Maintained by Dennis Irorere. Last updated 29 days ago.
datageospatiallocationopendataosmosmdataoverturemaps
10.0 match 15 stars 4.80 score 14 scripts
weecology
LDATS:Latent Dirichlet Allocation Coupled with Time Series Analyses
Combines Latent Dirichlet Allocation (LDA) and Bayesian multinomial time series methods in a two-stage analysis to quantify dynamics in high-dimensional temporal data. LDA decomposes multivariate data into lower-dimension latent groupings, whose relative proportions are modeled using generalized Bayesian time series models that include abrupt changepoints and smooth dynamics. The methods are described in Blei et al. (2003) <doi:10.1162/jmlr.2003.3.4-5.993>, Western and Kleykamp (2004) <doi:10.1093/pan/mph023>, Venables and Ripley (2002, ISBN-13:978-0387954578), and Christensen et al. (2018) <doi:10.1002/ecy.2373>.
Maintained by Juniper L. Simonis. Last updated 5 years ago.
changepointldaparallel-temperingportalsoftmax
6.9 match 25 stars 6.93 score 45 scriptsmazamascience
AirMonitor:Air Quality Data Analysis
Utilities for working with hourly air quality monitoring data with a focus on small particulates (PM2.5). A compact data model is structured as a list with two dataframes. A 'meta' dataframe contains spatial and measuring device metadata associated with deployments at known locations. A 'data' dataframe contains a 'datetime' column followed by columns of measurements associated with each "device-deployment". Algorithms to calculate NowCast and the associated Air Quality Index (AQI) are defined at the US Environmental Projection Agency AirNow program: <https://document.airnow.gov/technical-assistance-document-for-the-reporting-of-daily-air-quailty.pdf>.
Maintained by Jonathan Callahan. Last updated 6 months ago.
7.2 match 7 stars 6.57 score 178 scripts
hriebl
lmls:Gaussian Location-Scale Regression
The Gaussian location-scale regression model is a multi-predictor model with explanatory variables for the mean (= location) and the standard deviation (= scale) of a response variable. This package implements maximum likelihood and Markov chain Monte Carlo (MCMC) inference (using algorithms from Girolami and Calderhead (2011) <doi:10.1111/j.1467-9868.2010.00765.x> and Nesterov (2009) <doi:10.1007/s10107-007-0149-x>), a parametric bootstrap algorithm, and diagnostic plots for the model class.
Maintained by Hannes Riebl. Last updated 4 months ago.
10.1 match 3 stars 4.65 score 15 scriptsbioc
MOMA:Multi Omic Master Regulator Analysis
This package implements the inference of candidate master regulator proteins from multi-omics' data (MOMA) algorithm, as well as ancillary analysis and visualization functions.
Maintained by Sunny Jones. Last updated 5 months ago.
softwarenetworkenrichmentnetworkinferencenetworkfeatureextractionclusteringfunctionalgenomicstranscriptomicssystemsbiology
7.6 match 6 stars 6.19 score 13 scripts
freezenik
bamlss:Bayesian Additive Models for Location, Scale, and Shape (and Beyond)
Infrastructure for estimating probabilistic distributional regression models in a Bayesian framework. The distribution parameters may capture location, scale, shape, etc. and every parameter may depend on complex additive terms (fixed, random, smooth, spatial, etc.) similar to a generalized additive model. The conceptual and computational framework is introduced in Umlauf, Klein, Zeileis (2019) <doi:10.1080/10618600.2017.1407325> and the R package in Umlauf, Klein, Simon, Zeileis (2021) <doi:10.18637/jss.v100.i04>.
Maintained by Nikolaus Umlauf. Last updated 5 months ago.
8.1 match 1 stars 5.76 score 239 scripts 5 dependents
mountainmath
cancensus:Access, Retrieve, and Work with Canadian Census Data and Geography
Integrated, convenient, and uniform access to Canadian Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready tidy data frames and spatial data in multiple formats, as well as convenience functions for working with Census variables, variable hierarchies, and region selection. API keys are freely available with free registration at <https://censusmapper.ca/api>. Census data and boundary geometries are reproduced and distributed on an "as is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006; 2011; 2016; 2021).
Maintained by Dmitry Shkolnik. Last updated 1 years ago.
5.3 match 82 stars 8.80 score 414 scripts
javlacalle
tsoutliers:Detection of Outliers in Time Series
Detection of outliers in time series following the Chen and Liu (1993) <DOI:10.2307/2290724> procedure. Innovational outliers, additive outliers, level shifts, temporary changes and seasonal level shifts are considered.
Maintained by Javier Lรณpez-de-Lacalle. Last updated 1 years ago.
9.7 match 5 stars 4.79 score 5 dependentsropensci
CoordinateCleaner:Automated Cleaning of Occurrence Records from Biological Collections
Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) <doi:10.1111/2041-210X.13152>.
Maintained by Alexander Zizka. Last updated 1 years ago.
4.3 match 82 stars 10.93 score 306 scripts 3 dependentselipousson
bcpss:Baltimore City Public Schools
Provides access to demographic, enrollment, and survey data on Baltimore City Public School System (BCPSS).
Maintained by Eli Pousson. Last updated 1 years ago.
13.3 match 3 stars 3.48 score 5 scriptsbioc
surfaltr:Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr
Cell surface proteins form a major fraction of the druggable proteome and can be used for tissue-specific delivery of oligonucleotide/cell-based therapeutics. Alternatively spliced surface protein isoforms have been shown to differ in their subcellular localization and/or their transmembrane (TM) topology. Surface proteins are hydrophobic and remain difficult to study thereby necessitating the use of TM topology prediction methods such as TMHMM and Phobius. However, there exists a need for bioinformatic approaches to streamline batch processing of isoforms for comparing and visualizing topologies. To address this gap, we have developed an R package, surfaltr. It pairs inputted isoforms, either known alternatively spliced or novel, with their APPRIS annotated principal counterparts, predicts their TM topologies using TMHMM or Phobius, and generates a customizable graphical output. Further, surfaltr facilitates the prioritization of biologically diverse isoform pairs through the incorporation of three different ranking metrics and through protein alignment functions. Citations for programs mentioned here can be found in the vignette.
Maintained by Pooja Gangras. Last updated 5 months ago.
softwarevisualizationdatarepresentationsplicedalignmentalignmentmultiplesequencealignmentmultiplecomparison
11.5 match 4.00 score 2 scripts
modeloriented
auditor:Model Audit - Verification, Validation, and Error Analysis
Provides an easy to use unified interface for creating validation plots for any model. The 'auditor' helps to avoid repetitive work consisting of writing code needed to create residual plots. This visualizations allow to asses and compare the goodness of fit, performance, and similarity of models.
Maintained by Alicja Gosiewska. Last updated 1 years ago.
classificationerror-analysisexplainable-artificial-intelligencemachine-learningmodel-validationregression-modelsresidualsxai
5.3 match 58 stars 8.76 score 94 scripts 2 dependents
osgeo
rgrass:Interface Between 'GRASS' Geographical Information System and 'R'
An interface between the 'GRASS' geographical information system ('GIS') and 'R', based on starting 'R' from within the 'GRASS' 'GIS' environment, or running a free-standing 'R' session in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the 'R' command line. The original interface package for 'GRASS 5' (2000-2010) is described in Bivand (2000) <doi:10.1016/S0098-3004(00)00057-1> and Bivand (2001) <https://www.r-project.org/conferences/DSC-2001/Proceedings/Bivand.pdf>. This was succeeded by 'spgrass6' for 'GRASS 6' (2006-2016) and 'rgrass7' for 'GRASS 7' (2015-present). The 'rgrass' package modernizes the interface for 'GRASS 8' while still permitting the use of 'GRASS 7'.
Maintained by Steven Pawley. Last updated 23 days ago.
5.0 match 28 stars 9.23 score 91 scripts 2 dependents
ediorg
ecocomDP:Tools to Create, Use, and Convert ecocomDP Data
Work with the Ecological Community Data Design Pattern. 'ecocomDP' is a flexible data model for harmonizing ecological community surveys, in a research question agnostic format, from source data published across repositories, and with methods that keep the derived data up-to-date as the underlying sources change. Described in O'Brien et al. (2021), <doi:10.1016/j.ecoinf.2021.101374>.
Maintained by Colin Smith. Last updated 7 months ago.
5.5 match 32 stars 8.22 score 77 scriptscran
ICS:Tools for Exploring Multivariate Data via ICS/ICA
Implementation of Tyler, Critchley, Duembgen and Oja's (JRSS B, 2009, <doi:10.1111/j.1467-9868.2009.00706.x>) and Oja, Sirkia and Eriksson's (AJS, 2006, <https://www.ajs.or.at/index.php/ajs/article/view/vol35,%20no2%263%20-%207>) method of two different scatter matrices to obtain an invariant coordinate system or independent components, depending on the underlying assumptions.
Maintained by Klaus Nordhausen. Last updated 1 years ago.
8.7 match 5.21 score 17 dependents
csids
csdata:Structural Data for Norway
Datasets relating to population in municipalities, municipality/county matching, and how different municipalities have merged/redistricted over time from 2006 to 2024.
Maintained by Richard Aubrey White. Last updated 6 months ago.
7.8 match 5.78 score 6 scripts 2 dependentsbioc
CrispRVariants:Tools for counting and visualising mutations in a target location
CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.
Maintained by Helen Lindsay. Last updated 5 months ago.
immunooncologycrisprgenomicvariationvariantdetectiongeneticvariabilitydatarepresentationvisualizationsequencing
8.1 match 5.51 score 32 scripts
spatstat
spatstat.geom:Geometrical Functionality of the 'spatstat' Family
Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)
Maintained by Adrian Baddeley. Last updated 2 days ago.
classes-and-objectsdistance-calculationgeometrygeometry-processingimagesmensurationplottingpoint-patternsspatial-dataspatial-data-analysis
3.7 match 7 stars 12.11 score 241 scripts 227 dependentstidyverse
purrr:Functional Programming Tools
A complete and consistent functional programming toolkit for R.
Maintained by Hadley Wickham. Last updated 1 months ago.
2.0 match 1.3k stars 22.12 score 59k scripts 6.9k dependents
psegaert
mrfDepth:Depth Measures in Multivariate, Regression and Functional Settings
Tools to compute depth measures and implementations of related tasks such as outlier detection, data exploration and classification of multivariate, regression and functional data.
Maintained by Jakob Raymaekers. Last updated 6 years ago.
8.9 match 3 stars 4.99 score 72 scripts 3 dependentsbioc
AnnotationHub:Client to access AnnotationHub resources
This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
infrastructuredataimportguithirdpartyclientcore-packageu24ca289073
3.2 match 17 stars 13.89 score 2.7k scripts 102 dependents
chjackson
a2bcovid:Inferring COVID-19 Transmission Events from Sequence and Location Data
A tool which combines genome sequence and the locations of infected individuals, using a statistical and evolutionary model, to estimate the likelihood that transmission occurred between particular individuals, and then to identify clusters of infections. It is currently designed to apply to COVID-19 infection dynamics on hospital wards.
Maintained by Chris Illingworth. Last updated 3 years ago.
13.9 match 3 stars 3.18 scoretidyverse
ggplot2:Create Elegant Data Visualisations Using the Grammar of Graphics
A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.
Maintained by Thomas Lin Pedersen. Last updated 9 days ago.
data-visualisationvisualisation
1.8 match 6.6k stars 25.10 score 645k scripts 7.5k dependents
martin3141
spant:MR Spectroscopy Analysis Tools
Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Maintained by Martin Wilson. Last updated 30 days ago.
brainmrimrsmrshubspectroscopyfortran
5.1 match 25 stars 8.52 score 81 scripts
obrl-soil
h3jsr:Access Uber's H3 Library
Provides access to Uber's H3 library for geospatial indexing via its JavaScript transpile 'h3-js' <https://github.com/uber/h3-js> and 'V8' <https://github.com/jeroen/v8>.
Maintained by Lauren OBrien. Last updated 1 years ago.
discrete-global-gridsh3spatial-indexing
5.2 match 67 stars 8.39 score 205 scripts 4 dependentsbioc
ORFik:Open Reading Frames in Genomics
R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.
Maintained by Haakon Tjeldnes. Last updated 28 days ago.
immunooncologysoftwaresequencingriboseqrnaseqfunctionalgenomicscoveragealignmentdataimportcpp
4.1 match 33 stars 10.63 score 115 scripts 2 dependents
epiforecasts
epinowcast:Flexible Hierarchical Nowcasting
Tools to enable flexible and efficient hierarchical nowcasting of right-truncated epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes. Nowcasting, in this context, is gaining situational awareness using currently available observations and the reporting patterns of historical observations. This can be useful when tracking the spread of infectious disease in real-time: without nowcasting, changes in trends can be obfuscated by partial reporting or their detection may be delayed due to the use of simpler methods like truncation. While the package has been designed with epidemiological applications in mind, it could be applied to any set of right-truncated time-series count data.
Maintained by Sam Abbott. Last updated 11 months ago.
cmdstanreffective-reproduction-number-estimationepidemiologyinfectious-disease-surveillancenowcastingoutbreak-analysispandemic-preparednessreal-time-infectious-disease-modellingstan
5.5 match 61 stars 7.88 score 65 scripts
alexkowa
EnvStats:Package for Environmental Statistics, Including US EPA Guidance
Graphical and statistical analyses of environmental data, with focus on analyzing chemical concentrations and physical parameters, usually in the context of mandated environmental monitoring. Major environmental statistical methods found in the literature and regulatory guidance documents, with extensive help that explains what these methods do, how to use them, and where to find them in the literature. Numerous built-in data sets from regulatory guidance documents and environmental statistics literature. Includes scripts reproducing analyses presented in the book "EnvStats: An R Package for Environmental Statistics" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4, <doi:10.1007/978-1-4614-8456-1>).
Maintained by Alexander Kowarik. Last updated 17 days ago.
3.4 match 26 stars 12.80 score 2.4k scripts 46 dependents
lbb220
GWmodel:Geographically-Weighted Models
Techniques from a particular branch of spatial statistics,termed geographically-weighted (GW) models. GW models suit situations when data are not described well by some global model, but where there are spatial regions where a suitably localised calibration provides a better description. 'GWmodel' includes functions to calibrate: GW summary statistics (Brunsdon et al., 2002)<doi: 10.1016/s0198-9715(01)00009-6>, GW principal components analysis (Harris et al., 2011)<doi: 10.1080/13658816.2011.554838>, GW discriminant analysis (Brunsdon et al., 2007)<doi: 10.1111/j.1538-4632.2007.00709.x> and various forms of GW regression (Brunsdon et al., 1996)<doi: 10.1111/j.1538-4632.1996.tb00936.x>; some of which are provided in basic and robust (outlier resistant) forms.
Maintained by Binbin Lu. Last updated 6 months ago.
6.8 match 18 stars 6.38 score 266 scripts 4 dependentscran
metRology:Support for Metrological Applications
Provides classes and calculation and plotting functions for metrology applications, including measurement uncertainty estimation and inter-laboratory metrology comparison studies.
Maintained by Stephen L R Ellison. Last updated 2 months ago.
9.1 match 5 stars 4.77 score 223 scripts 7 dependents
epinowcast
epinowcast:Flexible Hierarchical Nowcasting
Tools to enable flexible and efficient hierarchical nowcasting of right-truncated epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes. Nowcasting, in this context, is gaining situational awareness using currently available observations and the reporting patterns of historical observations. This can be useful when tracking the spread of infectious disease in real-time: without nowcasting, changes in trends can be obfuscated by partial reporting or their detection may be delayed due to the use of simpler methods like truncation. While the package has been designed with epidemiological applications in mind, it could be applied to any set of right-truncated time-series count data.
Maintained by Sam Abbott. Last updated 11 months ago.
cmdstanreffective-reproduction-number-estimationepidemiologyinfectious-disease-surveillancenowcastingoutbreak-analysispandemic-preparednessreal-time-infectious-disease-modellingstan
5.5 match 61 stars 7.79 score 71 scriptsinlabru-org
inlabru:Bayesian Latent Gaussian Modelling using INLA and Extensions
Facilitates spatial and general latent Gaussian modeling using integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>). Additionally, extends the GAM-like model class to more general nonlinear predictor expressions, and implements a log Gaussian Cox process likelihood for modeling univariate and spatial point processes based on ecological survey data. Model components are specified with general inputs and mapping methods to the latent variables, and the predictors are specified via general R expressions, with separate expressions for each observation likelihood model in multi-likelihood models. A prediction method based on fast Monte Carlo sampling allows posterior prediction of general expressions of the latent variables. Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019) <doi:10.1111/2041-210X.13168>.
Maintained by Finn Lindgren. Last updated 4 days ago.
3.4 match 96 stars 12.62 score 832 scripts 6 dependents
nowosad
spDataLarge:Large datasets for spatial analysis
Large datasets for spatial analysis. The data from this package could be retrived using the spData package.
Maintained by Jakub Nowosad. Last updated 5 months ago.
7.0 match 27 stars 6.15 score 1.2k scripts 1 dependents
kjhealy
gssrdoc:Document General Social Survey Variable
The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.
Maintained by Kieran Healy. Last updated 11 months ago.
18.7 match 2.28 score 38 scripts
evanodell
ukpolice:Download Data on UK Police and Crime
Downloads data from the 'UK Police' public data API, the full docs of which are available at <https://data.police.uk/docs/>. Includes data on police forces and police force areas, crime reports, and the use of stop-and-search powers.
Maintained by Evan Odell. Last updated 4 years ago.
api-clientcrimepolicepolice-apiuk
8.1 match 7 stars 5.16 score 41 scriptsbioc
ramwas:Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
A complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association analysis with respect to phenotypes of interest while correcting for top PCs and known covariates, (6) annotation of significant findings, and (7) multi-marker analysis (methylation risk score) using elastic net. Additionally, RaMWAS include tools for joint analysis of methlyation and genotype data. This work is published in Bioinformatics, Shabalin et al. (2018) <doi:10.1093/bioinformatics/bty069>.
Maintained by Andrey A Shabalin. Last updated 5 months ago.
dnamethylationsequencingqualitycontrolcoveragepreprocessingnormalizationbatcheffectprincipalcomponentdifferentialmethylationvisualization
6.9 match 10 stars 6.08 score 85 scripts
jonathanlees
Rquake:Seismic Hypocenter Determination
Non-linear inversion for hypocenter estimation and analysis of seismic data collected continuously, or in trigger mode. The functions organize other functions from 'RSEIS' and 'GEOmap' to help researchers pick, locate, and store hypocenters for detailed seismic investigation. Error ellipsoids and station influence are estimated via jackknife analysis. References include Iversen, E. S., and J. M. Lees (1996)<doi:10.1785/BSSA0860061853>.
Maintained by Jonathan M. Lees. Last updated 1 years ago.
23.8 match 1.76 score 57 scriptsbnosac
crfsuite:Conditional Random Fields for Labelling Sequential Data in Natural Language Processing
Wraps the 'CRFsuite' library <https://github.com/chokkan/crfsuite> allowing users to fit a Conditional Random Field model and to apply it on existing data. The focus of the implementation is in the area of Natural Language Processing where this R package allows you to easily build and apply models for named entity recognition, text chunking, part of speech tagging, intent recognition or classification of any category you have in mind. Next to training, a small web application is included in the package to allow you to easily construct training data.
Maintained by Jan Wijffels. Last updated 2 years ago.
chunkingconditional-random-fieldscrfcrfsuitedata-scienceintent-classificationnatural-language-processingnernlpcpp
6.6 match 63 stars 6.34 score 35 scriptsr-forge
RobExtremes:Optimally Robust Estimation for Extreme Value Distributions
Optimally robust estimation for extreme value distributions using S4 classes and methods (based on packages 'distr', 'distrEx', 'distrMod', 'RobAStBase', and 'ROptEst'); the underlying theoretic results can be found in Ruckdeschel and Horbenko, (2013 and 2012), \doi{10.1080/02331888.2011.628022} and \doi{10.1007/s00184-011-0366-4}.
Maintained by Peter Ruckdeschel. Last updated 2 months ago.
11.3 match 3.67 score 39 scripts
r-tmap
tmaptools:Thematic Map Tools
Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.
Maintained by Martijn Tennekes. Last updated 2 months ago.
3.5 match 42 stars 11.67 score 1.8k scripts 26 dependents
edwindj
sdcSpatial:Statistical Disclosure Control for Spatial Data
Privacy protected raster maps can be created from spatial point data. Protection methods include smoothing of dichotomous variables by de Jonge and de Wolf (2016) <doi:10.1007/978-3-319-45381-1_9>, continuous variables by de Wolf and de Jonge (2018) <doi:10.1007/978-3-319-99771-1_23>, suppressing revealing values and a generalization of the quad tree method by Suรฑรฉ, Rovira, Ibรกรฑez and Farrรฉ (2017) <doi:10.2901/EUROSTAT.C2017.001>.
Maintained by Edwin de Jonge. Last updated 2 days ago.
8.7 match 8 stars 4.75 score 14 scripts
lanedrew
ldmppr:Estimate and Simulate from Location Dependent Marked Point Processes
A suite of tools for estimating, assessing model fit, simulating from, and visualizing location dependent marked point processes characterized by regularity in the pattern. You provide a reference marked point process, a set of raster images containing location specific covariates, and select the estimation algorithm and type of mark model. 'ldmppr' estimates the process and mark models and allows you to check the appropriateness of the model using a variety of diagnostic tools. Once a satisfactory model fit is obtained, you can simulate from the model and visualize the results. Documentation for the package 'ldmppr' is available in the form of a vignette.
Maintained by Lane Drew. Last updated 20 days ago.
8.2 match 1 stars 5.00 score 2 scriptsbioc
ShortRead:FASTQ input and manipulation
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.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp
3.4 match 8 stars 12.08 score 1.8k scripts 49 dependents
hypertidy
ceramic:Download Online Imagery Tiles
Download imagery tiles to a standard cache and load the data into raster objects. Facilities for 'AWS' terrain <https://registry.opendata.aws/terrain-tiles/> terrain and 'Mapbox' <https://www.mapbox.com/> servers are provided.
Maintained by Michael Sumner. Last updated 1 years ago.
6.3 match 92 stars 6.44 score 121 scripts
rorynolan
strex:Extra String Manipulation Functions
There are some things that I wish were easier with the 'stringr' or 'stringi' packages. The foremost of these is the extraction of numbers from strings. 'stringr' and 'stringi' make you figure out the regular expression for yourself; 'strex' takes care of this for you. There are many other handy functionalities in 'strex'. Contributions to this package are encouraged; it is intended as a miscellany of string manipulation functions that cannot be found in 'stringi' or 'stringr'.
Maintained by Rory Nolan. Last updated 6 months ago.
3.8 match 41 stars 10.59 score 1.2k scripts 18 dependentsr-forge
distrEx:Extensions of Package 'distr'
Extends package 'distr' by functionals, distances, and conditional distributions.
Maintained by Matthias Kohl. Last updated 2 months ago.
6.0 match 6.68 score 107 scripts 17 dependentsusepa
elevatr:Access Elevation Data from Various APIs
Several web services are available that provide access to elevation data. This package provides access to many of those services and returns elevation data either as an 'sf' simple features object from point elevation services or as a 'raster' object from raster elevation services. In future versions, 'elevatr' will drop support for 'raster' and will instead return 'terra' objects. Currently, the package supports access to the Amazon Web Services Terrain Tiles <https://registry.opendata.aws/terrain-tiles/>, the Open Topography Global Datasets API <https://opentopography.org/developers/>, and the USGS Elevation Point Query Service <https://apps.nationalmap.gov/epqs/>.
Maintained by Jeffrey Hollister. Last updated 6 months ago.
digital-elevation-modelelevation-dataelevatrepamapzen-elevation-servicer-language
3.6 match 206 stars 11.11 score 1.3k scripts 3 dependents
ohdsi
PatientLevelPrediction:Develop Clinical Prediction Models Using the Common Data Model
A user friendly way to create patient level prediction models using the Observational Medical Outcomes Partnership Common Data Model. Given a cohort of interest and an outcome of interest, the package can use data in the Common Data Model to build a large set of features. These features can then be used to fit a predictive model with a number of machine learning algorithms. This is further described in Reps (2017) <doi:10.1093/jamia/ocy032>.
Maintained by Egill Fridgeirsson. Last updated 9 days ago.
3.7 match 190 stars 10.85 score 297 scriptsbioc
VariantAnnotation:Annotation of Genetic Variants
Annotate variants, compute amino acid coding changes, predict coding outcomes.
Maintained by Bioconductor Package Maintainer. Last updated 2 months ago.
dataimportsequencingsnpannotationgeneticsvariantannotationcurlbzip2xz-utilszlib
3.5 match 11.39 score 1.9k scripts 152 dependents
icarda-git
QBMS:Query the Breeding Management System(s)
This R package assists breeders in linking data systems with their analytic pipelines, a crucial step in digitizing breeding processes. It supports querying and retrieving phenotypic and genotypic data from systems like 'EBS' <https://ebs.excellenceinbreeding.org/>, 'BMS' <https://bmspro.io>, 'BreedBase' <https://breedbase.org>, and 'GIGWA' <https://github.com/SouthGreenPlatform/Gigwa2> (using 'BrAPI' <https://brapi.org> calls). Extra helper functions support environmental data sources, including 'TerraClimate' <https://www.climatologylab.org/terraclimate.html> and 'FAO' 'HWSDv2' <https://gaez.fao.org/pages/hwsd> soil database.
Maintained by Khaled Al-Shamaa. Last updated 6 months ago.
5.1 match 8 stars 7.85 score 33 scripts 1 dependentsinbo
camtrapdp:Read and Manipulate Camera Trap Data Packages
Read and manipulate Camera Trap Data Packages ('Camtrap DP'). 'Camtrap DP' (<https://camtrap-dp.tdwg.org>) is a data exchange format for camera trap data. With 'camtrapdp' you can read, filter and transform data (including to Darwin Core) before further analysis in e.g. 'camtraptor' or 'camtrapR'.
Maintained by Peter Desmet. Last updated 10 days ago.
7.0 match 7 stars 5.67 score 12 scriptscran
MARVEL:Revealing Splicing Dynamics at Single-Cell Resolution
Alternative splicing represents an additional and underappreciated layer of complexity underlying gene expression profiles. Nevertheless, there remains hitherto a paucity of software to investigate splicing dynamics at single-cell resolution. 'MARVEL' enables splicing analysis of single-cell RNA-sequencing data generated from plate- and droplet-based library preparation methods.
Maintained by Sean Wen. Last updated 2 years ago.
14.6 match 2.71 score 51 scripts
harrelfe
Hmisc:Harrell Miscellaneous
Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.
Maintained by Frank E Harrell Jr. Last updated 9 hours ago.
2.3 match 210 stars 17.61 score 17k scripts 750 dependents
urbananalyst
dodgr:Distances on Directed Graphs
Distances on dual-weighted directed graphs using priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>). Weighted directed graphs have weights from A to B which may differ from those from B to A. Dual-weighted directed graphs have two sets of such weights. A canonical example is a street network to be used for routing in which routes are calculated by weighting distances according to the type of way and mode of transport, yet lengths of routes must be calculated from direct distances.
Maintained by Mark Padgham. Last updated 6 days ago.
distanceopenstreetmaproutershortest-pathsstreet-networkscpp
3.4 match 129 stars 11.53 score 229 scripts 4 dependents
rkoenker
quantreg:Quantile Regression
Estimation and inference methods for models for conditional quantile functions: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also now included. See Koenker, R. (2005) Quantile Regression, Cambridge U. Press, <doi:10.1017/CBO9780511754098> and Koenker, R. et al. (2017) Handbook of Quantile Regression, CRC Press, <doi:10.1201/9781315120256>.
Maintained by Roger Koenker. Last updated 7 days ago.
2.8 match 18 stars 13.93 score 2.6k scripts 1.5k dependents
ggobi
tourr:Tour Methods for Multivariate Data Visualisation
Implements geodesic interpolation and basis generation functions that allow you to create new tour methods from R.
Maintained by Dianne Cook. Last updated 17 days ago.
3.5 match 65 stars 11.17 score 426 scripts 9 dependents
dsy109
mixtools:Tools for Analyzing Finite Mixture Models
Analyzes finite mixture models for various parametric and semiparametric settings. This includes mixtures of parametric distributions (normal, multivariate normal, multinomial, gamma), various Reliability Mixture Models (RMMs), mixtures-of-regressions settings (linear regression, logistic regression, Poisson regression, linear regression with changepoints, predictor-dependent mixing proportions, random effects regressions, hierarchical mixtures-of-experts), and tools for selecting the number of components (bootstrapping the likelihood ratio test statistic, mixturegrams, and model selection criteria). Bayesian estimation of mixtures-of-linear-regressions models is available as well as a novel data depth method for obtaining credible bands. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772 and the Chan Zuckerberg Initiative: Essential Open Source Software for Science (Grant No. 2020-255193).
Maintained by Derek Young. Last updated 9 months ago.
mixture-modelsmixture-of-expertssemiparametric-regression
3.4 match 20 stars 11.34 score 1.4k scripts 56 dependents
pbs-software
PBSmapping:Mapping Fisheries Data and Spatial Analysis Tools
This software has evolved from fisheries research conducted at the Pacific Biological Station (PBS) in 'Nanaimo', British Columbia, Canada. It extends the R language to include two-dimensional plotting features similar to those commonly available in a Geographic Information System (GIS). Embedded C code speeds algorithms from computational geometry, such as finding polygons that contain specified point events or converting between longitude-latitude and Universal Transverse Mercator (UTM) coordinates. Additionally, we include 'C++' code developed by Angus Johnson for the 'Clipper' library, data for a global shoreline, and other data sets in the public domain. Under the user's R library directory '.libPaths()', specifically in './PBSmapping/doc', a complete user's guide is offered and should be consulted to use package functions effectively.
Maintained by Rowan Haigh. Last updated 6 months ago.
3.8 match 11 stars 10.29 score 652 scripts 9 dependents
hzhanghenry
RCircos:Circos 2D Track Plot
A simple and flexible way to generate Circos 2D track plot images for genomic data visualization is implemented in this package. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.
Maintained by Hongen Zhang. Last updated 3 years ago.
5.3 match 6 stars 7.21 score 298 scripts 3 dependents
walkerke
mapboxapi:R Interface to 'Mapbox' Web Services
Includes support for 'Mapbox' Navigation APIs, including directions, isochrones, and route optimization; the Search API for forward and reverse geocoding; the Maps API for interacting with 'Mapbox' vector tilesets and visualizing 'Mapbox' maps in R; and 'Mapbox Tiling Service' and 'tippecanoe' for generating map tiles. See <https://docs.mapbox.com/api/> for more information about the 'Mapbox' APIs.
Maintained by Kyle Walker. Last updated 2 months ago.
5.0 match 112 stars 7.61 score 304 scriptsrstudio
shiny:Web Application Framework for R
Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.
Maintained by Winston Chang. Last updated 13 days ago.
reactiverstudioshinyweb-appweb-development
1.8 match 5.4k stars 21.28 score 108k scripts 1.8k dependentsr-forge
RobLox:Optimally Robust Influence Curves and Estimators for Location and Scale
Functions for the determination of optimally robust influence curves and estimators in case of normal location and/or scale (see Chapter 8 in Kohl (2005) <https://epub.uni-bayreuth.de/839/2/DissMKohl.pdf>).
Maintained by Matthias Kohl. Last updated 2 months ago.
8.7 match 4.40 score 70 scripts 1 dependents
rammkripa
weed:Wrangler for Emergency Events Database
Makes research involving EMDAT and related datasets easier. These Datasets are manually filled and have several formatting and compatibility issues. Weed aims to resolve these with its functions.
Maintained by Ram Kripa. Last updated 1 years ago.
em-datemergency-events-databaseweed
12.7 match 2 stars 3.00 score 6 scriptstidyverse
tidyr:Tidy Messy Data
Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).
Maintained by Hadley Wickham. Last updated 13 days ago.
1.7 match 1.4k stars 22.88 score 168k scripts 5.5k dependentsfishr-core-team
FSA:Simple Fisheries Stock Assessment Methods
A variety of simple fish stock assessment methods.
Maintained by Derek H. Ogle. Last updated 2 months ago.
fishfisheriesfisheries-managementfisheries-stock-assessmentpopulation-dynamicsstock-assessment
3.4 match 68 stars 11.08 score 1.7k scripts 6 dependents
satijalab
Seurat:Tools for Single Cell Genomics
A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Maintained by Paul Hoffman. Last updated 1 years ago.
human-cell-atlassingle-cell-genomicssingle-cell-rna-seqcpp
2.3 match 2.4k stars 16.86 score 50k scripts 73 dependentstidymodels
recipes:Preprocessing and Feature Engineering Steps for Modeling
A recipe prepares your data for modeling. We provide an extensible framework for pipeable sequences of feature engineering steps provides preprocessing tools to be applied to data. Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting processed output can then be used as inputs for statistical or machine learning models.
Maintained by Max Kuhn. Last updated 6 days ago.
2.0 match 584 stars 18.71 score 7.2k scripts 380 dependents
