Showing 73 of total 73 results (show query)
melff
memisc:Management of Survey Data and Presentation of Analysis Results
An infrastructure for the management of survey data including value labels, definable missing values, recoding of variables, production of code books, and import of (subsets of) 'SPSS' and 'Stata' files is provided. Further, the package allows to produce tables and data frames of arbitrary descriptive statistics and (almost) publication-ready tables of regression model estimates, which can be exported to 'LaTeX' and HTML.
Maintained by Martin Elff. Last updated 9 days ago.
4.8 match 46 stars 12.34 score 1.2k scripts 13 dependents
bioc
BiocParallel:Bioconductor facilities for parallel evaluation
This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.
Maintained by Martin Morgan. Last updated 24 days ago.
infrastructurebioconductor-packagecore-packageu24ca289073cpp
3.2 match 67 stars 17.40 score 7.3k scripts 1.1k dependentsbioc
LOLA:Locus overlap analysis for enrichment of genomic ranges
Provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This makes it possible to do automated enrichment analysis for genomic region sets, thus facilitating interpretation of functional genomics and epigenomics data.
Maintained by Nathan Sheffield. Last updated 5 months ago.
genesetenrichmentgeneregulationgenomeannotationsystemsbiologyfunctionalgenomicschipseqmethylseqsequencing
5.6 match 76 stars 9.34 score 160 scriptsbioc
S4Vectors:Foundation of vector-like and list-like containers in Bioconductor
The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).
Maintained by Hervé Pagès. Last updated 1 months ago.
infrastructuredatarepresentationbioconductor-packagecore-package
3.0 match 18 stars 16.05 score 1.0k scripts 1.9k 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 1 months ago.
infrastructuredatarepresentationbioconductor-packagecore-package
3.0 match 22 stars 15.09 score 2.1k scripts 1.8k dependentsbioc
BiocGenerics:S4 generic functions used in Bioconductor
The package defines many S4 generic functions used in Bioconductor.
Maintained by Hervé Pagès. Last updated 1 months ago.
infrastructurebioconductor-packagecore-package
3.0 match 12 stars 14.22 score 612 scripts 2.2k dependentsbioc
CoreGx:Classes and Functions to Serve as the Basis for Other 'Gx' Packages
A collection of functions and classes which serve as the foundation for our lab's suite of R packages, such as 'PharmacoGx' and 'RadioGx'. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future 'Gx' suite programs. Major features include a 'CoreSet' class, from which 'RadioSet' and 'PharmacoSet' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) <doi:10.1093/bioinformatics/btv723>. Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) <doi:10.1101/449793>.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
softwarepharmacogenomicsclassificationsurvival
6.4 match 6.53 score 63 scripts 6 dependents
cran
flexmix:Flexible Mixture Modeling
A general framework for finite mixtures of regression models using the EM algorithm is implemented. The E-step and all data handling are provided, while the M-step can be supplied by the user to easily define new models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering.
Maintained by Bettina Gruen. Last updated 15 days ago.
5.0 match 5 stars 8.19 score 113 dependentsbioc
hermes:Preprocessing, analyzing, and reporting of RNA-seq data
Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed `RNA-seq` data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from `BioMart`. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and 'DESeq2` as well as voom differential expression analyses are available.
Maintained by Daniel Sabanés Bové. Last updated 5 months ago.
rnaseqdifferentialexpressionnormalizationpreprocessingqualitycontrolrna-seqstatistical-engineering
5.0 match 11 stars 7.77 score 48 scripts 1 dependentsbioc
ncdfFlow:ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
Provides HDF5 storage based methods and functions for manipulation of flow cytometry data.
Maintained by Mike Jiang. Last updated 2 months ago.
immunooncologyflowcytometryzlibcpp
5.0 match 7.56 score 96 scripts 11 dependents
a-maldet
labelmachine:Make Labeling of R Data Sets Easy
Assign meaningful labels to data frame columns. 'labelmachine' manages your label assignment rules in 'yaml' files and makes it easy to use the same labels in multiple projects.
Maintained by Adrian Maldet. Last updated 5 years ago.
6.9 match 7 stars 5.26 score 13 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
3.0 match 8 stars 12.11 score 1.8k scripts 50 dependents
rstudio
promises:Abstractions for Promise-Based Asynchronous Programming
Provides fundamental abstractions for doing asynchronous programming in R using promises. Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also attending to something else. Semantics are similar to 'JavaScript' promises, but with a syntax that is idiomatic R.
Maintained by Joe Cheng. Last updated 1 months ago.
1.9 match 204 stars 17.10 score 688 scripts 2.6k dependentsbioc
gDRutils:A package with helper functions for processing drug response data
This package contains utility functions used throughout the gDR platform to fit data, manipulate data, and convert and validate data structures. This package also has the necessary default constants for gDR platform. Many of the functions are utilized by the gDRcore package.
Maintained by Arkadiusz Gladki. Last updated 2 days ago.
4.1 match 2 stars 7.40 score 3 scripts 3 dependents
r-forge
tm:Text Mining Package
A framework for text mining applications within R.
Maintained by Kurt Hornik. Last updated 23 days ago.
2.3 match 12.96 score 14k scripts 101 dependents
r-lib
lintr:A 'Linter' for R Code
Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with 'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text', 'Atom' and 'Visual Studio Code'.
Maintained by Michael Chirico. Last updated 6 days ago.
1.7 match 1.2k stars 17.00 score 916 scripts 33 dependents
hojsgaard
doBy:Groupwise Statistics, LSmeans, Linear Estimates, Utilities
Utility package containing: 1) Facilities for working with grouped data: 'do' something to data stratified 'by' some variables. 2) LSmeans (least-squares means), general linear estimates. 3) Restrict functions to a smaller domain. 4) Miscellaneous other utilities.
Maintained by Søren Højsgaard. Last updated 2 days ago.
1.8 match 1 stars 14.94 score 3.2k scripts 939 dependents
flr
FLCore:Core Package of FLR, Fisheries Modelling in R
Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flr-project.org/>.
Maintained by Iago Mosqueira. Last updated 7 days ago.
fisheriesflrfisheries-modelling
3.0 match 16 stars 8.78 score 956 scripts 23 dependents
smart-cities-accelerator
onlineforecast:Forecast Modelling for Online Applications
A framework for fitting adaptive forecasting models. Provides a way to use forecasts as input to models, e.g. weather forecasts for energy related forecasting. The models can be fitted recursively and can easily be setup for updating parameters when new data arrives. See the included vignettes, the website <https://onlineforecasting.org> and the paper "onlineforecast: An R package for adaptive and recursive forecasting" <https://journal.r-project.org/articles/RJ-2023-031/>.
Maintained by Peder Bacher. Last updated 1 years ago.
7.6 match 3 stars 3.28 score 16 scriptsbioc
rols:An R interface to the Ontology Lookup Service
The rols package is an interface to the Ontology Lookup Service (OLS) to access and query hundred of ontolgies directly from R.
Maintained by Laurent Gatto. Last updated 5 months ago.
immunooncologysoftwareannotationmassspectrometrygo
3.0 match 11 stars 8.30 score 89 scripts 5 dependents
renkun-ken
rlist:A Toolbox for Non-Tabular Data Manipulation
Provides a set of functions for data manipulation with list objects, including mapping, filtering, grouping, sorting, updating, searching, and other useful functions. Most functions are designed to be pipeline friendly so that data processing with lists can be chained.
Maintained by Kun Ren. Last updated 2 years ago.
1.8 match 204 stars 13.69 score 2.2k scripts 123 dependents
rdpeng
filehash:Simple Key-Value Database
Implements a simple key-value style database where character string keys are associated with data values that are stored on the disk. A simple interface is provided for inserting, retrieving, and deleting data from the database. Utilities are provided that allow 'filehash' databases to be treated much like environments and lists are already used in R. These utilities are provided to encourage interactive and exploratory analysis on large datasets. Three different file formats for representing the database are currently available and new formats can easily be incorporated by third parties for use in the 'filehash' framework.
Maintained by Roger D. Peng. Last updated 2 years ago.
3.0 match 24 stars 8.16 score 78 scripts 11 dependentsbioc
flowWorkspace:Infrastructure for representing and interacting with gated and ungated cytometry data sets.
This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.
Maintained by Greg Finak. Last updated 8 days ago.
immunooncologyflowcytometrydataimportpreprocessingdatarepresentationzlibopenblascpp
3.0 match 7.89 score 576 scripts 10 dependents
statnet
statnet.common:Common R Scripts and Utilities Used by the Statnet Project Software
Non-statistical utilities used by the software developed by the Statnet Project. They may also be of use to others.
Maintained by Pavel N. Krivitsky. Last updated 24 days ago.
2.0 match 8 stars 11.42 score 197 scripts 148 dependents
winvector
wrapr:Wrap R Tools for Debugging and Parametric Programming
Tools for writing and debugging R code. Provides: '%.>%' dot-pipe (an 'S3' configurable pipe), unpack/to (R style multiple assignment/return), 'build_frame()'/'draw_frame()' ('data.frame' example tools), 'qc()' (quoting concatenate), ':=' (named map builder), 'let()' (converts non-standard evaluation interfaces to parametric standard evaluation interfaces, inspired by 'gtools::strmacro()' and 'base::bquote()'), and more.
Maintained by John Mount. Last updated 2 years ago.
2.0 match 137 stars 11.11 score 390 scripts 12 dependents
robinhankin
freealg:The Free Algebra
The free algebra in R with non-commuting indeterminates. Uses 'disordR' discipline (Hankin, 2022, <doi:10.48550/ARXIV.2210.03856>). To cite the package in publications please use Hankin (2022) <doi:10.48550/ARXIV.2211.04002>.
Maintained by Robin K. S. Hankin. Last updated 3 days ago.
3.0 match 3 stars 7.07 score 10 dependentsbioc
MetaboAnnotation:Utilities for Annotation of Metabolomics Data
High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.
Maintained by Johannes Rainer. Last updated 3 months ago.
infrastructuremetabolomicsmassspectrometryannotationmass-spectromtry
3.0 match 15 stars 6.98 score 35 scriptsrobinhankin
mvp:Fast Symbolic Multivariate Polynomials
Fast manipulation of symbolic multivariate polynomials using the 'Map' class of the Standard Template Library. The package uses print and coercion methods from the 'mpoly' package but offers speed improvements. It is comparable in speed to the 'spray' package for sparse arrays, but retains the symbolic benefits of 'mpoly'. To cite the package in publications, use Hankin 2022 <doi:10.48550/ARXIV.2210.15991>. Uses 'disordR' discipline.
Maintained by Robin K. S. Hankin. Last updated 1 days ago.
3.0 match 9 stars 6.83 score 36 scripts 2 dependentsrobinhankin
clifford:Arbitrary Dimensional Clifford Algebras
A suite of routines for Clifford algebras, using the 'Map' class of the Standard Template Library. Canonical reference: Hestenes (1987, ISBN 90-277-1673-0, "Clifford algebra to geometric calculus"). Special cases including Lorentz transforms, quaternion multiplication, and Grassmann algebra, are discussed. Vignettes presenting conformal geometric algebra, quaternions and split quaternions, dual numbers, and Lorentz transforms are included. The package follows 'disordR' discipline.
Maintained by Robin K. S. Hankin. Last updated 30 days ago.
3.0 match 5 stars 6.73 score 4 scripts
turtletopia
aurrera:Wrap an Interable in a Progress Bar
Allows a simple creation of progress bars by wrapping the iterated object in 'pb()'.
Maintained by Laura Bakala. Last updated 2 years ago.
10.0 match 2 stars 2.00 score 3 scripts
ropensci
RNeXML:Semantically Rich I/O for the 'NeXML' Format
Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
Maintained by Carl Boettiger. Last updated 10 months ago.
metadatanexmlphylogeneticslinked-data
2.0 match 13 stars 9.92 score 100 scripts 19 dependents
insightsengineering
rbmi:Reference Based Multiple Imputation
Implements standard and reference based multiple imputation methods for continuous longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular, this package supports deterministic conditional mean imputation and jackknifing as described in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum likelihood imputation as described in von Hippel and Bartlett (2021) <doi: 10.1214/20-STS793>.
Maintained by Isaac Gravestock. Last updated 21 days ago.
2.3 match 18 stars 8.78 score 33 scripts 1 dependentsrobinhankin
disordR:Non-Ordered Vectors
Functionality for manipulating values of associative maps. The package is a dependency for mvp-type packages that use the STL map class: it traps plausible idiom that is ill-defined (implementation-specific) and returns an informative error, rather than returning a possibly incorrect result. To cite the package in publications please use Hankin (2022) <doi:10.48550/ARXIV.2210.03856>.
Maintained by Robin K. S. Hankin. Last updated 4 months ago.
3.0 match 1 stars 6.59 score 20 dependents
thothorn
modeltools:Tools and Classes for Statistical Models
A collection of tools to deal with statistical models. The functionality is experimental and the user interface is likely to change in the future. The documentation is rather terse, but packages `coin' and `party' have some working examples. However, if you find the implemented ideas interesting we would be very interested in a discussion of this proposal. Contributions are more than welcome!
Maintained by Torsten Hothorn. Last updated 5 years ago.
3.0 match 6.56 score 84 scripts 254 dependents
tommyjones
textmineR:Functions for Text Mining and Topic Modeling
An aid for text mining in R, with a syntax that should be familiar to experienced R users. Provides a wrapper for several topic models that take similarly-formatted input and give similarly-formatted output. Has additional functionality for analyzing and diagnostics for topic models.
Maintained by Tommy Jones. Last updated 2 years ago.
1.8 match 106 stars 10.83 score 310 scripts 7 dependents
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.
1.8 match 20 stars 10.59 score 980 scripts 69 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
1.8 match 67 stars 9.94 score 436 scripts 2 dependents
kollerma
robustlmm:Robust Linear Mixed Effects Models
Implements the Robust Scoring Equations estimator to fit linear mixed effects models robustly. Robustness is achieved by modification of the scoring equations combined with the Design Adaptive Scale approach.
Maintained by Manuel Koller. Last updated 1 years ago.
2.0 match 28 stars 8.79 score 138 scriptsbioc
scRNAseqApp:A single-cell RNAseq Shiny app-package
The scRNAseqApp is a Shiny app package designed for interactive visualization of single-cell data. It is an enhanced version derived from the ShinyCell, repackaged to accommodate multiple datasets. The app enables users to visualize data containing various types of information simultaneously, facilitating comprehensive analysis. Additionally, it includes a user management system to regulate database accessibility for different users.
Maintained by Jianhong Ou. Last updated 14 days ago.
visualizationsinglecellrnaseqinteractive-visualizationsmultiple-usersshiny-appssingle-cell-rna-seq
3.0 match 4 stars 5.78 score 3 scripts
branchlab
metasnf:Meta Clustering with Similarity Network Fusion
Framework to facilitate patient subtyping with similarity network fusion and meta clustering. The similarity network fusion (SNF) algorithm was introduced by Wang et al. (2014) in <doi:10.1038/nmeth.2810>. SNF is a data integration approach that can transform high-dimensional and diverse data types into a single similarity network suitable for clustering with minimal loss of information from each initial data source. The meta clustering approach was introduced by Caruana et al. (2006) in <doi:10.1109/ICDM.2006.103>. Meta clustering involves generating a wide range of cluster solutions by adjusting clustering hyperparameters, then clustering the solutions themselves into a manageable number of qualitatively similar solutions, and finally characterizing representative solutions to find ones that are best for the user's specific context. This package provides a framework to easily transform multi-modal data into a wide range of similarity network fusion-derived cluster solutions as well as to visualize, characterize, and validate those solutions. Core package functionality includes easy customization of distance metrics, clustering algorithms, and SNF hyperparameters to generate diverse clustering solutions; calculation and plotting of associations between features, between patients, and between cluster solutions; and standard cluster validation approaches including resampled measures of cluster stability, standard metrics of cluster quality, and label propagation to evaluate generalizability in unseen data. Associated vignettes guide the user through using the package to identify patient subtypes while adhering to best practices for unsupervised learning.
Maintained by Prashanth S Velayudhan. Last updated 3 days ago.
bioinformaticsclusteringmetaclusteringsnf
1.8 match 8 stars 8.21 score 30 scriptsbioc
ChIPseqR:Identifying Protein Binding Sites in High-Throughput Sequencing Data
ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.
Maintained by Peter Humburg. Last updated 5 months ago.
3.0 match 4.70 score 1 scripts
snoweye
pbdMPI:R Interface to MPI for HPC Clusters (Programming with Big Data Project)
A simplified, efficient, interface to MPI for HPC clusters. It is a derivation and rethinking of the Rmpi package. pbdMPI embraces the prevalent parallel programming style on HPC clusters. Beyond the interface, a collection of functions for global work with distributed data and resource-independent RNG reproducibility is included. It is based on S4 classes and methods.
Maintained by Wei-Chen Chen. Last updated 6 months ago.
1.9 match 2 stars 7.11 score 179 scripts 3 dependentsbioc
multiHiCcompare:Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner.
Maintained by Mikhail Dozmorov. Last updated 5 months ago.
softwarehicsequencingnormalization
1.8 match 9 stars 7.30 score 37 scripts 2 dependents
kharchenkolab
pagoda2:Single Cell Analysis and Differential Expression
Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/pagoda2>. The size of the 'p2data' package is approximately 6 MB.
Maintained by Evan Biederstedt. Last updated 1 years ago.
scrna-seqsingle-cellsingle-cell-rna-seqtranscriptomicsopenblascppopenmp
1.6 match 222 stars 8.00 score 282 scriptsbioc
XDE:XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
Multi-level model for cross-study detection of differential gene expression.
Maintained by Robert Scharpf. Last updated 5 months ago.
microarraydifferentialexpressioncpp
3.0 match 4.20 score 10 scripts
rickhelmus
RDCOMClient:R-DCOM client
Provides dynamic client-side access to (D)COM applications from within R.
Maintained by Duncan Temple Lang. Last updated 1 years ago.
3.0 match 3.90 score 315 scripts
munterfi
eRTG3D:Empirically Informed Random Trajectory Generation in 3-D
Creates realistic random trajectories in a 3-D space between two given fix points, so-called conditional empirical random walks (CERWs). The trajectory generation is based on empirical distribution functions extracted from observed trajectories (training data) and thus reflects the geometrical movement characteristics of the mover. A digital elevation model (DEM), representing the Earth's surface, and a background layer of probabilities (e.g. food sources, uplift potential, waterbodies, etc.) can be used to influence the trajectories. Unterfinger M (2018). "3-D Trajectory Simulation in Movement Ecology: Conditional Empirical Random Walk". Master's thesis, University of Zurich. <https://www.geo.uzh.ch/dam/jcr:6194e41e-055c-4635-9807-53c5a54a3be7/MasterThesis_Unterfinger_2018.pdf>. Technitis G, Weibel R, Kranstauber B, Safi K (2016). "An algorithm for empirically informed random trajectory generation between two endpoints". GIScience 2016: Ninth International Conference on Geographic Information Science, 9, online. <doi:10.5167/uzh-130652>.
Maintained by Merlin Unterfinger. Last updated 3 years ago.
3dbirdsconditional-empirical-random-walkgliding-and-soaringmachine-learningmovement-ecologyrandom-trajectory-generatorrandom-walksimulationtrajectory-generation
2.0 match 6 stars 5.71 score 19 scripts
markbravington
mvbutils:General utilities, workspace organization, code and docu editing, live package maintenance, etc
Hierarchical workspace tree, code editing and backup, easy package prep, editing of packages while loaded, per-object lazy-loading, easy documentation, macro functions, and miscellaneous utilities. Needed by debug package.
Maintained by Mark V. Bravington. Last updated 4 days ago.
1.8 match 6.53 score 138 scripts 18 dependents
reidt03
RadOnc:Analytical Tools for Radiation Oncology
Designed for the import, analysis, and visualization of dosimetric and volumetric data in Radiation Oncology, the tools herein enable import of dose-volume histogram information from multiple treatment planning system platforms and 3D structural representations and dosimetric information from 'DICOM-RT' files. These tools also enable subsequent visualization and statistical analysis of these data.
Maintained by Reid F. Thompson. Last updated 2 months ago.
3.0 match 8 stars 3.78 score 19 scripts
benmbutler
powdR:Full Pattern Summation of X-Ray Powder Diffraction Data
Full pattern summation of X-ray powder diffraction data as described in Chipera and Bish (2002) <doi:10.1107/S0021889802017405> and Butler and Hillier (2021) <doi:10.1016/j.cageo.2020.104662>. Derives quantitative estimates of crystalline and amorphous phase concentrations in complex mixtures.
Maintained by Benjamin Butler. Last updated 3 years ago.
2.0 match 12 stars 5.56 score 30 scriptskharchenkolab
sccore:Core Utilities for Single-Cell RNA-Seq
Core utilities for single-cell RNA-seq data analysis. Contained within are utility functions for working with differential expression (DE) matrices and count matrices, a collection of functions for manipulating and plotting data via 'ggplot2', and functions to work with cell graphs and cell embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP <doi:10.21105/joss.00861>, collapsing vertices of each cluster in the graph, and propagating graph labels.
Maintained by Evan Biederstedt. Last updated 1 years ago.
1.7 match 12 stars 6.44 score 36 scripts 9 dependents
martingmayer
preventr:An Implementation of the PREVENT and Pooled Cohort Equations
Implements the American Heart Association Predicting Risk of cardiovascular disease EVENTs (PREVENT) equations from Khan SS, Matsushita K, Sang Y, and colleagues (2023) <doi:10.1161/CIRCULATIONAHA.123.067626>, with optional comparison with their de facto predecessor, the Pooled Cohort Equations from the American Heart Association and American College of Cardiology (2013) <doi:10.1161/01.cir.0000437741.48606.98> and the revision to the Pooled Cohort Equations from Yadlowsky and colleagues (2018) <doi:10.7326/M17-3011>.
Maintained by Martin Mayer. Last updated 2 months ago.
2.0 match 11 stars 5.34 score 4 scriptsbioc
oligoClasses:Classes for high-throughput arrays supported by oligo and crlmm
This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.
Maintained by Benilton Carvalho. Last updated 5 months ago.
1.8 match 5.85 score 93 scripts 17 dependents
kylebaron
mrgsim.parallel:Simulate with 'mrgsolve' in Parallel
Simulation from an 'mrgsolve' <https://cran.r-project.org/package=mrgsolve> model using a parallel backend. Input data sets are split (chunked) and simulated in parallel using mclapply() or future_lapply() <https://cran.r-project.org/package=future.apply>.
Maintained by Kyle Baron. Last updated 3 months ago.
2.0 match 5 stars 5.11 score 17 scriptsbioc
Streamer:Enabling stream processing of large files
Large data files can be difficult to work with in R, where data generally resides in memory. This package encourages a style of programming where data is 'streamed' from disk into R via a `producer' and through a series of `consumers' that, typically reduce the original data to a manageable size. The package provides useful Producer and Consumer stream components for operations such as data input, sampling, indexing, and transformation; see package?Streamer for details.
Maintained by Martin Morgan. Last updated 5 months ago.
3.0 match 3.30 score 2 scripts
etiennebacher
flir:Find and Fix Lints in R Code
Lints are code patterns that are not optimal because they are inefficient, forget corner cases, or less readable. 'flir' provides a small set of functions to detect those lints and automatically fix them. It builds on 'astgrepr', which itself uses the Rust crate 'ast-grep' to parse and navigate R code.
Maintained by Etienne Bacher. Last updated 18 days ago.
1.7 match 52 stars 5.74 score 1 scripts
revolutionanalytics
foreach:Provides Foreach Looping Construct
Support for the foreach looping construct. Foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.
Maintained by Folashade Daniel. Last updated 3 years ago.
0.5 match 54 stars 17.16 score 43k scripts 2.8k dependents
xoopr
ooplah:Helper Functions for Class Object-Oriented Programming
Helper functions for coding object-oriented programming with a focus on R6. Includes functions for assertions and testing, looping, and re-usable design patterns including Abstract and Decorator classes.
Maintained by Raphael Sonabend. Last updated 3 years ago.
2.0 match 7 stars 4.32 score 2 dependentsbioc
midasHLA:R package for immunogenomics data handling and association analysis
MiDAS is a R package for immunogenetics data transformation and statistical analysis. MiDAS accepts input data in the form of HLA alleles and KIR types, and can transform it into biologically meaningful variables, enabling HLA amino acid fine mapping, analyses of HLA evolutionary divergence, KIR gene presence, as well as validated HLA-KIR interactions. Further, it allows comprehensive statistical association analysis workflows with phenotypes of diverse measurement scales. MiDAS closes a gap between the inference of immunogenetic variation and its efficient utilization to make relevant discoveries related to T cell, Natural Killer cell, and disease biology.
Maintained by Maciej Migdał. Last updated 5 months ago.
cellbiologygeneticsstatisticalmethod
2.0 match 4.30 score 3 scripts
predictiveecology
pemisc:Miscellaneous Utilities Developed by the Predictive Ecology Group
Miscellaneous utilities developed by the Predictive Ecology Group (<http://predictiveecology.org>).
Maintained by Eliot J B McIntire. Last updated 3 months ago.
landscape-ecologysimulation-modeling
2.0 match 1 stars 3.83 score 3 scripts 5 dependentspredictiveecology
fireSenseUtils:Utilities for Working With the 'fireSense' Group of 'SpaDES' Modules
Utilities for working with the 'fireSense' group of 'SpaDES' modules.
Maintained by Eliot J B McIntire. Last updated 28 days ago.
1.7 match 1 stars 4.53 score 2 scripts
go-ski
clustra:Clustering Longitudinal Trajectories
Clusters longitudinal trajectories over time (can be unequally spaced, unequal length time series and/or partially overlapping series) on a common time axis. Performs k-means clustering on a single continuous variable measured over time, where each mean is defined by a thin plate spline fit to all points in a cluster. Distance is MSE across trajectory points to cluster spline. Provides graphs of derived cluster splines, silhouette plots, and Adjusted Rand Index evaluations of the number of clusters. Scales well to large data with multicore parallelism available to speed computation.
Maintained by George Ostrouchov. Last updated 3 months ago.
1.6 match 4.48 score 6 scripts
dvdscripter
ini:Read and Write '.ini' Files
Parse simple '.ini' configuration files to an structured list. Users can manipulate this resulting list with lapply() functions. This same structured list can be used to write back to file after modifications.
Maintained by David Valentim Dias. Last updated 7 years ago.
0.5 match 7 stars 10.48 score 219 scripts 417 dependents
ggrothendieck
gsubfn:Utilities for Strings and Function Arguments
The gsubfn function is like gsub but can take a replacement function or certain other objects instead of the replacement string. Matches and back references are input to the replacement function and replaced by the function output. gsubfn can be used to split strings based on content rather than delimiters and for quasi-perl-style string interpolation. The package also has facilities for translating formulas to functions and allowing such formulas in function calls instead of functions. This can be used with R functions such as apply, sapply, lapply, optim, integrate, xyplot, Filter and any other function that expects another function as an input argument or functions like cat or sql calls that may involve strings where substitution is desirable. There is also a facility for returning multiple objects from functions and a version of transform that allows the RHS to refer to LHS used in the same transform.
Maintained by G. Grothendieck. Last updated 7 years ago.
0.5 match 11 stars 10.58 score 872 scripts 76 dependents
vald
timetools:Seasonal/Sequential (Instants/Durations, Even or not) Time Series
Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time durations are handled. Both can be regularly or unevenly spaced (overlapping durations are allowed). Only POSIX* format are used for dates and times. The following classes are provided : 'POSIXcti', 'POSIXctp', 'TimeIntervalDataFrame', 'TimeInstantDataFrame', 'SubtimeDataFrame' ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
Maintained by Vladislav Navel. Last updated 2 years ago.
3.0 match 1.08 score 12 scripts
jluchman
domir:Tools to Support Relative Importance Analysis
Methods to apply decomposition-based relative importance analysis for R functions. This package supports the application of decomposition methods by providing 'lapply'- or 'Map'-like meta-functions that compute dominance analysis (Azen, R., & Budescu, D. V. (2003) <doi:10.1037/1082-989X.8.2.129>; Grömping, U. (2007) <doi:10.1198/000313007X188252>) an extension of Shapley value regression (Lipovetsky, S., & Conklin, M. (2001) <doi:10.1002/asmb.446>) based on the values returned from other functions.
Maintained by Joseph Luchman. Last updated 10 months ago.
dominance-analysisrelative-importanceshapley-valuevariable-importance
0.5 match 5 stars 5.75 score 30 scripts
rcannood
qsub:Running Commands Remotely on 'Gridengine' Clusters
Run lapply() calls in parallel by submitting them to 'gridengine' clusters using the 'qsub' command.
Maintained by Robrecht Cannoodt. Last updated 3 years ago.
0.6 match 9 stars 5.07 score 37 scripts
cmann3
eList:List Comprehension and Tools
Create list comprehensions (and other types of comprehension) similar to those in 'python', 'haskell', and other languages. List comprehension in 'R' converts a regular for() loop into a vectorized lapply() function. Support for looping with multiple variables, parallelization, and across non-standard objects included. Package also contains a variety of functions to help with list comprehension.
Maintained by Chris Mann. Last updated 4 years ago.
0.5 match 2 stars 4.48 score 9 scripts 1 dependents
xiaoran831213
fcp:Function Composition
A function composition operator to chain a series of calls into a single function, mimicking the math notion of (f o g o h)(x) = h(g(f(x))). Inspired by 'pipeOp' ('|>') since R4.1 and 'magrittr pipe' ('%>%'), the operator build a pipe without putting data through, which is best for anonymous function accepted by utilities such as apply() and lapply().
Maintained by Xiaoran Tong. Last updated 1 years ago.
0.5 match 2.00 score 3 scripts