Showing 30 of total 30 results (show query)
tidyverse
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 26 days ago.
4.8k stars 24.68 score 659k scripts 7.8k dependents
bioc
Biostrings:Efficient manipulation of biological strings
Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
Maintained by Hervé Pagès. Last updated 1 months ago.
sequencematchingalignmentsequencinggeneticsdataimportdatarepresentationinfrastructurebioconductor-packagecore-package
62 stars 17.77 score 8.6k scripts 1.2k dependentsbioc
ggtree:an R package for visualization of tree and annotation data
'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.
Maintained by Guangchuang Yu. Last updated 5 months ago.
alignmentannotationclusteringdataimportmultiplesequencealignmentphylogeneticsreproducibleresearchsoftwarevisualizationannotationsggplot2phylogenetic-trees
871 stars 16.83 score 5.1k scripts 109 dependentsbioc
IRanges:Foundation of integer range manipulation in Bioconductor
Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.
Maintained by Hervé Pagès. Last updated 2 months ago.
infrastructuredatarepresentationbioconductor-packagecore-package
22 stars 16.09 score 2.1k scripts 1.8k dependents
epiforecasts
EpiNow2:Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters
Estimates the time-varying reproduction number, rate of spread, and doubling time using a range of open-source tools (Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and current best practices (Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some of the limitations of naive implementations in a framework that is informed by community feedback and is actively supported.
Maintained by Sebastian Funk. Last updated 1 months ago.
backcalculationcovid-19gaussian-processesopen-sourcereproduction-numberstancpp
123 stars 11.86 score 210 scripts
berndbischl
BBmisc:Miscellaneous Helper Functions for B. Bischl
Miscellaneous helper functions for and from B. Bischl and some other guys, mainly for package development.
Maintained by Bernd Bischl. Last updated 2 years ago.
20 stars 10.65 score 980 scripts 68 dependents
cran
nlme:Linear and Nonlinear Mixed Effects Models
Fit and compare Gaussian linear and nonlinear mixed-effects models.
Maintained by R Core Team. Last updated 2 months ago.
6 stars 9.77 score 8.8k dependents
atlasoflivingaustralia
galah:Biodiversity Data from the GBIF Node Network
The Global Biodiversity Information Facility ('GBIF', <https://www.gbif.org>) sources data from an international network of data providers, known as 'nodes'. Several of these nodes - the "living atlases" (<https://living-atlases.gbif.org>) - maintain their own web services using software originally developed by the Atlas of Living Australia ('ALA', <https://www.ala.org.au>). 'galah' enables the R community to directly access data and resources hosted by 'GBIF' and its partner nodes.
Maintained by Martin Westgate. Last updated 2 months ago.
43 stars 9.17 score 275 scripts 1 dependents
r-hyperspec
hyperSpec:Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)
Comfortable ways to work with hyperspectral data sets, i.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra. The spectra can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f(wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.
Maintained by Claudia Beleites. Last updated 10 months ago.
data-wranglinghyperspectralimaginginfrarednmrramanspectroscopyuv-visxrf
16 stars 8.10 score 233 scripts 2 dependents
dipterix
dipsaus:A Dipping Sauce for Data Analysis and Visualizations
Works as an "add-on" to packages like 'shiny', 'future', as well as 'rlang', and provides utility functions. Just like dipping sauce adding flavors to potato chips or pita bread, 'dipsaus' for data analysis and visualizations adds handy functions and enhancements to popular packages. The goal is to provide simple solutions that are frequently asked for online, such as how to synchronize 'shiny' inputs without freezing the app, or how to get memory size on 'Linux' or 'MacOS' system. The enhancements roughly fall into these four categories: 1. 'shiny' input widgets; 2. high-performance computing using the 'future' package; 3. modify R calls and convert among numbers, strings, and other objects. 4. utility functions to get system information such like CPU chip-set, memory limit, etc.
Maintained by Zhengjia Wang. Last updated 5 days ago.
13 stars 8.02 score 85 scripts 3 dependents
biogenies
tidysq:Tidy Processing and Analysis of Biological Sequences
A tidy approach to analysis of biological sequences. All processing and data-storage functions are heavily optimized to allow the fastest and most efficient data storage.
Maintained by Dominik Rafacz. Last updated 3 months ago.
bioconductorbioinformaticsbiological-sequencesfastas3sequencestibbletidytidyversevctrscpp
40 stars 7.56 score 38 scripts
divdyn
divDyn:Diversity Dynamics using Fossil Sampling Data
Functions to describe sampling and diversity dynamics of fossil occurrence datasets (e.g. from the Paleobiology Database). The package includes methods to calculate range- and occurrence-based metrics of taxonomic richness, extinction and origination rates, along with traditional sampling measures. A powerful subsampling tool is also included that implements frequently used sampling standardization methods in a multiple bin-framework. The plotting of time series and the occurrence data can be simplified by the functions incorporated in the package, as well as other calculations, such as environmental affinities and extinction selectivity testing. Details can be found in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) <doi:10.1101/423780>.
Maintained by Adam T. Kocsis. Last updated 4 months ago.
diversityextinctionfossil-dataoccurrencesoriginationpaleobiologycpp
11 stars 6.48 score 137 scripts
eth-mds
ricu:Intensive Care Unit Data with R
Focused on (but not exclusive to) data sets hosted on PhysioNet (<https://physionet.org>), 'ricu' provides utilities for download, setup and access of intensive care unit (ICU) data sets. In addition to functions for running arbitrary queries against available data sets, a system for defining clinical concepts and encoding their representations in tabular ICU data is presented.
Maintained by Nicolas Bennett. Last updated 10 months ago.
39 stars 5.65 score 77 scripts
taddylab
distrom:Distributed Multinomial Regression
Fast distributed/parallel estimation for multinomial logistic regression via Poisson factorization and the 'gamlr' package. For details see: Taddy (2015, AoAS), Distributed Multinomial Regression, <arXiv:1311.6139>.
Maintained by Nelson Rayl. Last updated 8 months ago.
19 stars 5.58 score 44 scripts 3 dependents
edgarsantos-fernandez
SSNbayes:Bayesian Spatio-Temporal Analysis in Stream Networks
Fits Bayesian spatio-temporal models and makes predictions on stream networks using the approach by Santos-Fernandez, Edgar, et al. (2022)."Bayesian spatio-temporal models for stream networks" and Santos-Fernandez, Edgar, et al. (2023). "SSNbayes: An R Package for Bayesian Spatio-Temporal Modelling on Stream Networks". In these models, spatial dependence is captured using stream distance and flow connectivity, while temporal autocorrelation is modelled using vector autoregression methods.
Maintained by Edgar Santos-Fernandez. Last updated 2 months ago.
17 stars 5.41 score 6 scripts
rdoctaskforce
pkgcond:Classed Error and Warning Conditions
This provides utilities for creating classed error and warning conditions based on where the error originated.
Maintained by Andrew Redd. Last updated 4 years ago.
5 stars 5.19 score 41 scripts 5 dependentsdipterix
ravetools:Signal and Image Processing Toolbox for Analyzing Intracranial Electroencephalography Data
Implemented fast and memory-efficient Notch-filter, Welch-periodogram, discrete wavelet spectrogram for minutes of high-resolution signals, fast 3D convolution, image registration, 3D mesh manipulation; providing fundamental toolbox for intracranial Electroencephalography (iEEG) pipelines. Documentation and examples about 'RAVE' project are provided at <https://rave.wiki>, and the paper by John F. Magnotti, Zhengjia Wang, Michael S. Beauchamp (2020) <doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for details.
Maintained by Zhengjia Wang. Last updated 17 days ago.
3 stars 5.13 score 20 scripts 1 dependents
choi-phd
lordif:Logistic Ordinal Regression Differential Item Functioning using IRT
Performs analysis of Differential Item Functioning (DIF) for dichotomous and polytomous items using an iterative hybrid of ordinal logistic regression and item response theory (IRT) according to Choi, Gibbons, and Crane (2011) <doi:10.18637/jss.v039.i08>.
Maintained by Seung W. Choi. Last updated 3 months ago.
1 stars 5.12 score 35 scripts 1 dependents
dereckmezquita
stenographer:Flexible and Customisable Logging System
A comprehensive logging framework for R applications that provides hierarchical logging levels, database integration, and contextual logging capabilities. The package supports 'SQLite' storage for persistent logs, provides colour-coded console output for better readability, includes parallel processing support, and implements structured error reporting with 'JSON' formatting.
Maintained by Dereck Mezquita. Last updated 2 months ago.
3 stars 5.08 score 1 scripts
mbq
vistla:Detecting Influence Paths with Information Theory
Traces information spread through interactions between features, utilising information theory measures and a higher-order generalisation of the concept of widest paths in graphs. In particular, 'vistla' can be used to better understand the results of high-throughput biomedical experiments, by organising the effects of the investigated intervention in a tree-like hierarchy from direct to indirect ones, following the plausible information relay circuits. Due to its higher-order nature, 'vistla' can handle multi-modality and assign multiple roles to a single feature.
Maintained by Miron B. Kursa. Last updated 1 months ago.
4.70 score 3 scripts
peekxc
simplextree:Provides Tools for Working with General Simplicial Complexes
Provides an interface to a Simplex Tree data structure, which is a data structure aimed at enabling efficient manipulation of simplicial complexes of any dimension. The Simplex Tree data structure was originally introduced by Jean-Daniel Boissonnat and Clément Maria (2014) <doi:10.1007/s00453-014-9887-3>.
Maintained by Matt Piekenbrock. Last updated 1 years ago.
rcppsimplicial-complextopological-data-analysistopologycpp
15 stars 4.56 score 16 scripts 1 dependents
jmbarbone
fuj:Functions and Utilities for Jordan
Provides core functions and utilities for packages and other code developed by Jordan Mark Barbone.
Maintained by Jordan Mark Barbone. Last updated 20 days ago.
2 stars 4.48 score 8 scripts 1 dependents
setempler
miscset:Miscellaneous Tools Set
A collection of miscellaneous methods to simplify various tasks, including plotting, data.frame and matrix transformations, environment functions, regular expression methods, and string and logical operations, as well as numerical and statistical tools. Most of the methods are simple but useful wrappers of common base R functions, which extend S3 generics or provide default values for important parameters.
Maintained by Sven E. Templer. Last updated 8 years ago.
1 stars 4.40 score 50 scripts
wrathematics
kazaam:Tools for Tall Distributed Matrices
Many data science problems reduce to operations on very tall, skinny matrices. However, sometimes these matrices can be so tall that they are difficult to work with, or do not even fit into main memory. One strategy to deal with such objects is to distribute their rows across several processors. To this end, we offer an 'S4' class for tall, skinny, distributed matrices, called the 'shaq'. We also provide many useful numerical methods and statistics operations for operating on these distributed objects. The naming is a bit "tongue-in-cheek", with the class a play on the fact that 'Shaquille' 'ONeal' ('Shaq') is very tall, and he starred in the film 'Kazaam'.
Maintained by Drew Schmidt. Last updated 8 years ago.
3.82 score 133 scripts
certe-medical-epidemiology
certetoolbox:A Certe R Package for Miscellaneous Functions
A Certe R Package for miscellaneous functions that do not fit a dedicated package. This package also mitigates the 'vctrs' package by allowing numeric-character coercions. This package is part of the 'certedata' universe.
Maintained by Erwin E. A. Hassing. Last updated 9 days ago.
3.45 score 1 scripts 1 dependentsbioc
spikeLI:Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
SpikeLI is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006).
Maintained by Enrico Carlon. Last updated 5 months ago.
3.30 score
calbertsen
caMisc:Different Functions
More about what it does (maybe more than one line)
Maintained by Christoffer Moesgaard Albertsen. Last updated 9 months ago.
1.70 score
marco-geraci
pawacc:Physical Activity with Accelerometers
Functions to process, format and store ActiGraph GT1M and GT3X accelerometer data.
Maintained by Marco Geraci. Last updated 1 years ago.
1 stars 1.08 score 12 scripts