R-universe search: utility

henrikbengtsson

R.utils:Various Programming Utilities

Utility functions useful when programming and developing R packages.

Maintained by Henrik Bengtsson. Last updated 1 years ago.

45.7 match 63 stars 13.74 score 5.7k scripts 814 dependents

spatstat

spatstat.utils:Utility Functions for 'spatstat'

Contains utility functions for the 'spatstat' family of packages which may also be useful for other purposes.

Maintained by Adrian Baddeley. Last updated 3 days ago.

spatial-analysis spatial-data spatstat

47.2 match 5 stars 11.66 score 134 scripts 248 dependents

peterreichert

utility:Construct, Evaluate and Plot Value and Utility Functions

Construct and plot objective hierarchies and associated value and utility functions. Evaluate the values and utilities and visualize the results as colored objective hierarchies or tables. Visualize uncertainty by plotting median and quantile intervals within the nodes of objective hierarchies. Get numerical results of the evaluations in standard R data types for further processing.

Maintained by Peter Reichert. Last updated 2 years ago.

162.4 match 3.35 score 82 scripts 1 dependents

bioc

UCSC.utils:Low-level utilities to retrieve data from the UCSC Genome Browser

A set of low-level utilities to retrieve data from the UCSC Genome Browser. Most functions in the package access the data via the UCSC REST API but some of them query the UCSC MySQL server directly. Note that the primary purpose of the package is to support higher-level functionalities implemented in downstream packages like GenomeInfoDb or txdbmaker.

Maintained by Hervé Pagès. Last updated 2 months ago.

infrastructure genomeassembly annotation genomeannotation dataimport bioconductor-package core-package

44.2 match 1 stars 10.09 score 4 scripts 1.7k dependents

pecanproject

PEcAn.utils:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Rob Kooper. Last updated 3 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

37.5 match 216 stars 10.92 score 218 scripts 35 dependents

bioc

Rsamtools:Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

Maintained by Bioconductor Package Maintainer. Last updated 4 months ago.

dataimport sequencing coverage alignment qualitycontrol bioconductor-package core-package curl bzip2 xz-utils zlib cpp

24.8 match 28 stars 15.42 score 3.2k scripts 566 dependents

yulab-smu

yulab.utils:Supporting Functions for Packages Maintained by 'YuLab-SMU'

Miscellaneous functions commonly used by 'YuLab-SMU'.

Maintained by Guangchuang Yu. Last updated 4 days ago.

37.5 match 33 stars 9.94 score 21 scripts 228 dependents

alexanderrobitzsch

miceadds:Some Additional Multiple Imputation Functions, Especially for 'mice'

Contains functions for multiple imputation which complements existing functionality in R. In particular, several imputation methods for the mice package (van Buuren & Groothuis-Oudshoorn, 2011, <doi:10.18637/jss.v045.i03>) are implemented. Main features of the miceadds package include plausible value imputation (Mislevy, 1991, <doi:10.1007/BF02294457>), multilevel imputation for variables at any level or with any number of hierarchical and non-hierarchical levels (Grund, Luedtke & Robitzsch, 2018, <doi:10.1177/1094428117703686>; van Buuren, 2018, Ch.7, <doi:10.1201/9780429492259>), imputation using partial least squares (PLS) for high dimensional predictors (Robitzsch, Pham & Yanagida, 2016), nested multiple imputation (Rubin, 2003, <doi:10.1111/1467-9574.00217>), substantive model compatible imputation (Bartlett et al., 2015, <doi:10.1177/0962280214521348>), and features for the generation of synthetic datasets (Reiter, 2005, <doi:10.1111/j.1467-985X.2004.00343.x>; Nowok, Raab, & Dibben, 2016, <doi:10.18637/jss.v074.i11>).

Maintained by Alexander Robitzsch. Last updated 17 days ago.

missing-data multiple-imputation openblas cpp

36.8 match 16 stars 9.16 score 542 scripts 9 dependents

bioc

maftools:Summarize, Analyze and Visualize MAF Files

Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.

Maintained by Anand Mayakonda. Last updated 5 months ago.

datarepresentation dnaseq visualization drivermutation variantannotation featureextraction classification somaticmutation sequencing functionalgenomics survival bioinformatics cancer-genome-atlas cancer-genomics genomics maf-files tcga curl bzip2 xz-utils zlib

22.5 match 459 stars 14.63 score 948 scripts 18 dependents

bioc

basilisk.utils:Basilisk Installation Utilities

Implements utilities for installation of the basilisk package, primarily for creation of the underlying Conda instance. This allows us to avoid re-writing the same R code in both the configure script (for centrally administered R installations) and in the lazy installation mechanism (for distributed package binaries). It is highly unlikely that developers - or, heaven forbid, end-users! - will need to interact with this package directly; they should be using the basilisk package instead.

Maintained by Aaron Lun. Last updated 1 months ago.

infrastructure

44.7 match 7.24 score 9 scripts 40 dependents

kwb-r

kwb.utils:General Utility Functions Developed at KWB

This package contains some small helper functions that aim at improving the quality of code developed at Kompetenzzentrum Wasser gGmbH (KWB).

Maintained by Hauke Sonnenberg. Last updated 12 months ago.

40.5 match 8 stars 7.33 score 12 scripts 78 dependents

insightsengineering

ggplot2.utils:Selected Utilities Extending 'ggplot2'

Selected utilities, in particular 'geoms' and 'stats' functions, extending the 'ggplot2' package. This package imports functions from 'EnvStats' <doi:10.1007/978-1-4614-8456-1> by Millard (2013), 'ggpp' <https://CRAN.R-project.org/package=ggpp> by Aphalo et al. (2023) and 'ggstats' <doi:10.5281/zenodo.10183964> by Larmarange (2023), and then exports them. This package also contains modified code from 'ggquickeda' <https://CRAN.R-project.org/package=ggquickeda> by Mouksassi et al. (2023) for Kaplan-Meier lines and ticks additions to plots. All functions are tested to make sure that they work reliably.

Maintained by Daniel Sabanés Bové. Last updated 9 months ago.

43.1 match 6 stars 6.26 score 14 scripts

bioc

methylKit:DNA methylation analysis from high-throughput bisulfite sequencing results

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.

Maintained by Altuna Akalin. Last updated 17 days ago.

dnamethylation sequencing methylseq genome-biology methylation statistical-analysis visualization curl bzip2 xz-utils zlib cpp

22.5 match 220 stars 11.80 score 578 scripts 3 dependents

bnowok

synthpop:Generating Synthetic Versions of Sensitive Microdata for Statistical Disclosure Control

A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data. For a description of the implemented method see Nowok, Raab and Dibben (2016) <doi:10.18637/jss.v074.i11>.

Maintained by Beata Nowok. Last updated 3 years ago.

33.5 match 44 stars 7.85 score 536 scripts

bioc

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.

dataimport sequencing snp annotation genetics variantannotation curl bzip2 xz-utils zlib

22.5 match 11.39 score 1.9k scripts 152 dependents

bioc

Rhtslib:HTSlib high-throughput sequencing library as an R package

This package provides version 1.18 of the 'HTSlib' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib").

Maintained by Hervé Pagès. Last updated 13 days ago.

dataimport sequencing bioconductor-package core-package curl bzip2 xz-utils zlib

22.5 match 11 stars 11.25 score 3 scripts 591 dependents

cb4ds

DGEobj.utils:Differential Gene Expression (DGE) Analysis Utility Toolkit

Provides a function toolkit to facilitate reproducible RNA-Seq Differential Gene Expression (DGE) analysis (Law (2015) <doi:10.12688/f1000research.9005.3>). The tools include both analysis work-flow and utility functions: mapping/unit conversion, count normalization, accounting for unknown covariates, and more. This is a complement/cohort to the 'DGEobj' package that provides a flexible container to manage and annotate Differential Gene Expression analysis results.

Maintained by Connie Brett. Last updated 2 months ago.

45.9 match 2 stars 5.26 score 30 scripts 1 dependents

bioc

scPipe:Pipeline for single cell multi-omic data pre-processing

A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts from the fastq files and produces a feature count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.

Maintained by Shian Su. Last updated 3 months ago.

immunooncology software sequencing rnaseq geneexpression singlecell visualization sequencematching preprocessing qualitycontrol genomeannotation dataimport curl bzip2 xz-utils zlib cpp

22.5 match 68 stars 9.02 score 84 scripts

bioc

bamsignals:Extract read count signals from bam files

This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

Maintained by Johannes Helmuth. Last updated 5 months ago.

dataimport sequencing coverage alignment curl bzip2 xz-utils zlib cpp

22.5 match 15 stars 8.95 score 31 scripts 11 dependents

bioc

QuasR:Quantify and Annotate Short Reads in R

This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest. Read alignments are either generated through Rbowtie (data from DNA/ChIP/ATAC/Bis-seq experiments) or Rhisat2 (data from RNA-seq experiments that require spliced alignments), or can be provided in the form of bam files.

Maintained by Michael Stadler. Last updated 25 days ago.

genetics preprocessing sequencing chipseq rnaseq methylseq coverage alignment qualitycontrol immunooncology curl bzip2 xz-utils zlib cpp

22.5 match 6 stars 8.70 score 79 scripts 1 dependents

joshobrien

gdalUtilities:Wrappers for 'GDAL' Utilities Executables

R's 'sf' package ships with self-contained 'GDAL' executables, including a bare bones interface to several 'GDAL'-related utility programs collectively known as the 'GDAL utilities'. For each of those utilities, this package provides an R wrapper whose formal arguments closely mirror those of the 'GDAL' command line interface. The utilities operate on data stored in files and typically write their output to other files. Therefore, to process data stored in any of R's more common spatial formats (i.e. those supported by the 'sf' and 'terra' packages), first write them to disk, then process them with the package's wrapper functions before reading the outputted results back into R. GDAL function arguments introduced in GDAL version 3.5.2 or earlier are supported.

Maintained by Joshua OBrien. Last updated 2 years ago.

26.6 match 37 stars 7.09 score 252 scripts 6 dependents

bioc

csaw:ChIP-Seq Analysis with Windows

Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

Maintained by Aaron Lun. Last updated 2 months ago.

multiplecomparison chipseq normalization sequencing coverage genetics annotation differentialpeakcalling curl bzip2 xz-utils zlib cpp

22.5 match 8.32 score 498 scripts 7 dependents

r-forge

pems.utils:Portable Emissions (and Other Mobile) Measurement System Utilities

Utility functions for the handling, analysis and visualisation of data from portable emissions measurement systems ('PEMS') and other similar mobile activity monitoring devices. The package includes a dedicated 'pems' data class that manages many of the quality control, unit handling and data archiving issues that can hinder efforts to standardise 'PEMS' research.

Maintained by Karl Ropkins. Last updated 2 months ago.

openjdk

61.2 match 3.06 score 19 scripts

pbosetti

adas.utils:Design of Experiments and Factorial Plans for the ADAS Course, University of Trento, Italy

A number of functions to create and analyze factorial plans according to the Design of Experiments (DoE) approach, with the addition of some utility function to perform some statistical analyses.

Maintained by Paolo Bosetti. Last updated 3 months ago.

doe statistics

43.4 match 4.18 score 6 scripts

bioc

FLAMES:FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.

Maintained by Changqing Wang. Last updated 7 days ago.

rnaseq singlecell transcriptomics dataimport differentialsplicing alternativesplicing geneexpression longread zlib curl bzip2 xz-utils cpp

22.5 match 31 stars 7.95 score 12 scripts

natverse

nat.utils:File System Utility Functions for 'NeuroAnatomy Toolbox'

Utility functions that may be of general interest but are specifically required by the 'NeuroAnatomy Toolbox' ('nat'). Includes functions to provide a basic make style system to update files based on timestamp information, file locking and 'touch' utility. Convenience functions for working with file paths include 'abs2rel', 'split_path' and 'common_path'. Finally there are utility functions for working with 'zip' and 'gzip' files including integrity tests.

Maintained by Gregory Jefferis. Last updated 7 months ago.

nat neuroanatomy-toolbox

43.1 match 4.13 score 15 scripts 3 dependents

leslie-lu

lulab.utils:Supporting Functions Maintained by Zhen Lu

Miscellaneous functions commonly used by LuLab. This package aims to help more researchers on epidemiology to perform data management and visualization more efficiently.

Maintained by Zhen Lu. Last updated 5 months ago.

41.3 match 4.18 score 6 scripts

green-striped-gecko

dartR.base:Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism') and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT' (Diversity Arrays Technology), however, data from other sequencing platforms can be used once 'SNP' or related fragment presence/absence data from any source is imported. Genetic datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for a very compact storage of data and metadata. Functions are available for importing and exporting of 'SNP' and 'silicodart' data, for reporting on and filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility', maximum allele frequency). Additional functions are available for visualization (e.g. Principle Coordinate Analysis) and creating a spatial representation using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages. To install the other packages, we recommend to install the 'dartRverse' package, that supports the installation of all packages in the 'dartRverse'. If you want to cite 'dartR', you find the information by typing citation('dartR.base') in the console.

Maintained by Bernd Gruber. Last updated 14 days ago.

44.2 match 3.84 score 17 scripts 5 dependents

bioc

MsCoreUtils:Core Utils for Mass Spectrometry Data

MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning, baseline estimation), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...), misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.

Maintained by RforMassSpectrometry Package Maintainer. Last updated 6 days ago.

infrastructure proteomics massspectrometry metabolomics bioconductor mass-spectrometry utils

16.0 match 16 stars 10.52 score 41 scripts 71 dependents

nepem-ufsc

metan:Multi Environment Trials Analysis

Performs stability analysis of multi-environment trial data using parametric and non-parametric methods. Parametric methods includes Additive Main Effects and Multiplicative Interaction (AMMI) analysis by Gauch (2013) <doi:10.2135/cropsci2013.04.0241>, Ecovalence by Wricke (1965), Genotype plus Genotype-Environment (GGE) biplot analysis by Yan & Kang (2003) <doi:10.1201/9781420040371>, geometric adaptability index by Mohammadi & Amri (2008) <doi:10.1007/s10681-007-9600-6>, joint regression analysis by Eberhart & Russel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>, genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's (2004) method, power law residuals (POLAR) statistics by Doring et al. (2015) <doi:10.1016/j.fcr.2015.08.005>, scale-adjusted coefficient of variation by Doring & Reckling (2018) <doi:10.1016/j.eja.2018.06.007>, stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>, weighted average of absolute scores by Olivoto et al. (2019a) <doi:10.2134/agronj2019.03.0220>, and multi-trait stability index by Olivoto et al. (2019b) <doi:10.2134/agronj2019.03.0221>. Non-parametric methods includes superiority index by Lin & Binns (1988) <doi:10.4141/cjps88-018>, nonparametric measures of phenotypic stability by Huehn (1990) <doi:10.1007/BF00024241>, TOP third statistic by Fox et al. (1990) <doi:10.1007/BF00040364>. Functions for computing biometrical analysis such as path analysis, canonical correlation, partial correlation, clustering analysis, and tools for inspecting, manipulating, summarizing and plotting typical multi-environment trial data are also provided.

Maintained by Tiago Olivoto. Last updated 11 days ago.

17.0 match 2 stars 9.48 score 1.3k scripts 2 dependents

bioc

DiffBind:Differential Binding Analysis of ChIP-Seq Peak Data

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Maintained by Rory Stark. Last updated 2 months ago.

sequencing chipseq atacseq dnaseseq methylseq ripseq differentialpeakcalling differentialmethylation generegulation histonemodification peakdetection biomedicalinformatics cellbiology multiplecomparison normalization reportwriting epigenetics functionalgenomics curl bzip2 xz-utils zlib cpp

22.5 match 7.13 score 512 scripts 2 dependents

jl5000

tidyged.utils:Utilities to Manage GEDCOM Files Using Tidyverse Principles

Various utilities to manage and clean family tree GEDCOM files using tidy dataframes.

Maintained by Jamie Lendrum. Last updated 3 years ago.

40.9 match 3.88 score 6 scripts 1 dependents

bioc

TCGAutils:TCGA utility functions for data management

A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.

Maintained by Marcel Ramos. Last updated 3 months ago.

software workflowstep preprocessing dataimport bioconductor-package tcga u24ca289073 utilities

16.1 match 27 stars 9.66 score 210 scripts 10 dependents

rmi-pacta

pacta.portfolio.utils:pacta.portfolio.utils

For more information visit <https://rmi.org/>.

Maintained by CJ Yetman. Last updated 3 months ago.

climate-change pacta pactaverse sustainable-finance

36.7 match 1 stars 4.13 score 5 scripts 3 dependents

zilong-li

vcfppR:Rapid Manipulation of the Variant Call Format (VCF)

The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.

Maintained by Zilong Li. Last updated 4 days ago.

bioinformatics fastr htslib population-genetics population-genomics vcf vcf-data visulization libdeflate zlib bzip2 xz-utils curl cpp

22.5 match 13 stars 6.70 score 16 scripts

efinite

utile.tools:Summarize Data for Publication

Tools for formatting and summarizing data for outcomes research.

Maintained by Eric Finnesgard. Last updated 2 years ago.

37.5 match 5 stars 3.99 score 13 scripts 1 dependents

hesim-dev

hesim:Health Economic Simulation Modeling and Decision Analysis

A modular and computationally efficient R package for parameterizing, simulating, and analyzing health economic simulation models. The package supports cohort discrete time state transition models (Briggs et al. 1998) <doi:10.2165/00019053-199813040-00003>, N-state partitioned survival models (Glasziou et al. 1990) <doi:10.1002/sim.4780091106>, and individual-level continuous time state transition models (Siebert et al. 2012) <doi:10.1016/j.jval.2012.06.014>, encompassing both Markov (time-homogeneous and time-inhomogeneous) and semi-Markov processes. Decision uncertainty from a cost-effectiveness analysis is quantified with standard graphical and tabular summaries of a probabilistic sensitivity analysis (Claxton et al. 2005, Barton et al. 2008) <doi:10.1002/hec.985>, <doi:10.1111/j.1524-4733.2008.00358.x>. Use of C++ and data.table make individual-patient simulation, probabilistic sensitivity analysis, and incorporation of patient heterogeneity fast.

Maintained by Devin Incerti. Last updated 6 months ago.

health-economic-evaluation microsimulation simulation-modeling cpp

18.2 match 67 stars 8.12 score 41 scripts

bioc

deepSNV:Detection of subclonal SNVs in deep sequencing data.

This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters - such as local error rates and dispersion - and prior knowledge, e.g. from variation data bases such as COSMIC.

Maintained by Moritz Gerstung. Last updated 5 months ago.

geneticvariability snp sequencing genetics dataimport curl bzip2 xz-utils zlib cpp

22.5 match 6.53 score 38 scripts 1 dependents

nepem-ufsc

pliman:Tools for Plant Image Analysis

Tools for both single and batch image manipulation and analysis (Olivoto, 2022 <doi:10.1111/2041-210X.13803>) and phytopathometry (Olivoto et al., 2022 <doi:10.1007/S40858-021-00487-5>). The tools can be used for the quantification of leaf area, object counting, extraction of image indexes, shape measurement, object landmark identification, and Elliptical Fourier Analysis of object outlines (Claude (2008) <doi:10.1007/978-0-387-77789-4>). The package also provides a comprehensive pipeline for generating shapefiles with complex layouts and supports high-throughput phenotyping of RGB, multispectral, and hyperspectral orthomosaics. This functionality facilitates field phenotyping using UAV- or satellite-based imagery.

Maintained by Tiago Olivoto. Last updated 23 hours ago.

openblas fftw3 cpp openmp

21.5 match 10 stars 6.70 score 476 scripts

ycli1995

easy.utils:Frequently Used Functions for Easy R Programming

Some utility functions for validation and data manipulation. These functions can be helpful to reduce internal codes everywhere in package development.

Maintained by Yuchen Li. Last updated 27 days ago.

38.0 match 1 stars 3.78 score 1 dependents

mmaechler

sfsmisc:Utilities from 'Seminar fuer Statistik' ETH Zurich

Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich, some of which were ported from S-plus in the 1990s. For graphics, have pretty (Log-scale) axes eaxis(), an enhanced Tukey-Anscombe plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()', pretty arrows, etc. For robustness, have a robust F test and robust range(). For system support, notably on Linux, provides 'Sys.*()' functions with more access to system and CPU information. Finally, miscellaneous utilities such as simple efficient prime numbers, integer codes, Duplicated(), toLatex.numeric() and is.whole().

Maintained by Martin Maechler. Last updated 5 months ago.

13.1 match 11 stars 10.87 score 566 scripts 119 dependents

bioc

raer:RNA editing tools in R

Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.

Maintained by Kent Riemondy. Last updated 5 months ago.

multiplecomparison rnaseq singlecell sequencing coverage epitranscriptomics featureextraction annotation alignment bioconductor-package rna-seq-analysis single-cell-analysis single-cell-rna-seq curl bzip2 xz-utils zlib

22.5 match 8 stars 5.98 score 6 scripts

bioc

epialleleR:Fast, Epiallele-Aware Methylation Caller and Reporter

Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract and visualise methylation patterns and assess allele specificity of methylation.

Maintained by Oleksii Nikolaienko. Last updated 13 days ago.

dnamethylation epigenetics methylseq longread bioconductor dna-methylation epiallele next-generation-sequencing samtools curl bzip2 xz-utils zlib cpp

22.5 match 4 stars 5.94 score 5 scripts

cvxgrp

CVXR:Disciplined Convex Optimization

An object-oriented modeling language for disciplined convex programming (DCP) as described in Fu, Narasimhan, and Boyd (2020, <doi:10.18637/jss.v094.i14>). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution. Interfaces to solvers on CRAN and elsewhere are provided, both commercial and open source.

Maintained by Anqi Fu. Last updated 4 months ago.

cpp

10.3 match 207 stars 12.89 score 768 scripts 51 dependents

bioc

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.

infrastructure datarepresentation bioconductor-package core-package

8.2 match 18 stars 16.05 score 1.0k scripts 1.9k dependents

bioc

universalmotif:Import, Modify, and Export Motifs with R

Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.

Maintained by Benjamin Jean-Marie Tremblay. Last updated 4 months ago.

motifannotation motifdiscovery dataimport generegulation motif-analysis motif-enrichment-analysis sequence-logo cpp

11.7 match 28 stars 11.04 score 342 scripts 12 dependents

yrosseel

lavaan:Latent Variable Analysis

Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.

Maintained by Yves Rosseel. Last updated 9 hours ago.

factor-analysis growth-curve-models latent-variables missing-data multilevel-models multivariate-analysis path-analysis psychometrics statistical-modeling structural-equation-modeling

7.6 match 453 stars 16.85 score 8.4k scripts 216 dependents

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.

22.6 match 39 stars 5.65 score 77 scripts

bioc

diffHic:Differential Analysis of Hi-C Data

Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.

Maintained by Aaron Lun. Last updated 3 months ago.

multiplecomparison preprocessing sequencing coverage alignment normalization clustering hic curl bzip2 xz-utils zlib cpp

22.5 match 5.58 score 38 scripts

efinite

utile.visuals:Create Visuals for Publication

A set of functions to aid in the production of visuals in ggplot2.

Maintained by Eric Finnesgard. Last updated 2 years ago.

37.5 match 4 stars 3.30 score 7 scripts

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 6 days ago.

8.2 match 1 stars 14.94 score 3.2k scripts 939 dependents

tidyverse

lubridate:Make Dealing with Dates a Little Easier

Functions to work with date-times and time-spans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and time-span objects. The 'lubridate' package has a consistent and memorable syntax that makes working with dates easy and fun.

Maintained by Vitalie Spinu. Last updated 3 months ago.

date date-time

5.8 match 757 stars 20.95 score 135k scripts 1.9k 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 28 days ago.

10.6 match 8 stars 11.42 score 197 scripts 148 dependents

cldossantos

pacu:Precision Agriculture Computational Utilities

Support for a variety of commonly used precision agriculture operations. Includes functions to download and process raw satellite images from Sentinel-2 <https://documentation.dataspace.copernicus.eu/APIs/OData.html>. Includes functions that download vegetation index statistics for a given period of time, without the need to download the raw images <https://documentation.dataspace.copernicus.eu/APIs/SentinelHub/Statistical.html>. There are also functions to download and visualize weather data in a historical context. Lastly, the package also contains functions to process yield monitor data. These functions can build polygons around recorded data points, evaluate the overlap between polygons, clean yield data, and smooth yield maps.

Maintained by dos Santos Caio. Last updated 4 days ago.

17.6 match 14 stars 6.82 score 9 scripts

rinterface

shinyMobile:Mobile Ready 'shiny' Apps with Standalone Capabilities

Develop outstanding 'shiny' apps for 'iOS' and 'Android' as well as beautiful 'shiny' gadgets. 'shinyMobile' is built on top of the latest 'Framework7' template <https://framework7.io>. Discover 14 new input widgets (sliders, vertical sliders, stepper, grouped action buttons, toggles, picker, smart select, ...), 2 themes (light and dark), 12 new widgets (expandable cards, badges, chips, timelines, gauges, progress bars, ...) combined with the power of server-side notifications such as alerts, modals, toasts, action sheets, sheets (and more) as well as 3 layouts (single, tabs and split).

Maintained by David Granjon. Last updated 2 months ago.

android hacktoberfest2022 pwa shiny shinyapps template

10.0 match 409 stars 11.91 score 1.1k scripts 2 dependents

pedroguarderas

mau:Decision Models with Multi Attribute Utility Theory

Provides functions for the creation, evaluation and test of decision models based in Multi Attribute Utility Theory (MAUT). Can process and evaluate local risk aversion utilities for a set of indexes, compute utilities and weights for the whole decision tree defining the decision model and simulate weights employing Dirichlet distributions under addition constraints in weights. Also includes other rating analysis methods as for example the Colley, Offensive - Defensive ratings and the ranking aggregation with Borda count.

Maintained by Pedro Guarderas. Last updated 10 months ago.

decision-model utility

26.3 match 1 stars 4.52 score 11 scripts

lucasnell

jackalope:A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator

Simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina <https://www.illumina.com/> and Pacific Biosciences (PacBio) <https://www.pacb.com/> platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. 'jackalope' can simulate single, paired-end, or mate-pair Illumina reads, as well as PacBio reads. These simulations include sequencing errors, mapping qualities, multiplexing, and optical/polymerase chain reaction (PCR) duplicates. Simulating Illumina sequencing is based on ART by Huang et al. (2012) <doi:10.1093/bioinformatics/btr708>. PacBio sequencing simulation is based on SimLoRD by Stöcker et al. (2016) <doi:10.1093/bioinformatics/btw286>. All outputs can be written to standard file formats.

Maintained by Lucas A. Nell. Last updated 1 years ago.

zlib openblas curl bzip2 xz-utils cpp

22.5 match 8 stars 5.28 score 24 scripts

mlcollyer

RRPP:Linear Model Evaluation with Randomized Residuals in a Permutation Procedure

Linear model calculations are made for many random versions of data. Using residual randomization in a permutation procedure, sums of squares are calculated over many permutations to generate empirical probability distributions for evaluating model effects. Additionally, coefficients, statistics, fitted values, and residuals generated over many permutations can be used for various procedures including pairwise tests, prediction, classification, and model comparison. This package should provide most tools one could need for the analysis of high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.

Maintained by Michael Collyer. Last updated 27 days ago.

12.0 match 4 stars 9.84 score 173 scripts 7 dependents

qile0317

FastUtils:Fast, Readable Utility Functions

A wide variety of tools for general data analysis, wrangling, spelling, statistics, visualizations, package development, and more. All functions have vectorized implementations whenever possible. Exported names are designed to be readable, with longer names possessing short aliases.

Maintained by Qile Yang. Last updated 4 months ago.

scientific-computing utilities utility cpp

23.1 match 2 stars 4.95 score 2 scripts

bioc

podkat:Position-Dependent Kernel Association Test

This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.

Maintained by Ulrich Bodenhofer. Last updated 5 months ago.

genetics wholegenome annotation variantannotation sequencing dataimport curl bzip2 xz-utils zlib cpp

22.5 match 5.02 score 6 scripts

bioc

scuttle:Single-Cell RNA-Seq Analysis Utilities

Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.

Maintained by Aaron Lun. Last updated 5 months ago.

immunooncology singlecell rnaseq qualitycontrol preprocessing normalization transcriptomics geneexpression sequencing software dataimport openblas cpp

10.6 match 10.21 score 1.7k scripts 80 dependents

efinite

utile.tables:Build Tables for Publication

Functions for building customized ready-to-export tables for publication.

Maintained by Eric Finnesgard. Last updated 2 years ago.

37.5 match 1 stars 2.70 score 2 scripts

mschubert

narray:Subset- And Name-Aware Array Utility Functions

Stacking arrays according to dimension names, subset-aware splitting and mapping of functions, intersecting along arbitrary dimensions, converting to and from data.frames, and many other helper functions.

Maintained by Michael Schubert. Last updated 2 months ago.

array utility cpp

14.6 match 27 stars 6.91 score 10 scripts 10 dependents

bioc

h5vc:Managing alignment tallies using a hdf5 backend

This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files.

Maintained by Paul Theodor Pyl. Last updated 2 months ago.

curl bzip2 xz-utils zlib cpp

22.5 match 4.48 score 2 scripts

bioc

mitoClone2:Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

This package primarily identifies variants in mitochondrial genomes from BAM alignment files. It filters these variants to remove RNA editing events then estimates their evolutionary relationship (i.e. their phylogenetic tree) and groups single cells into clones. It also visualizes the mutations and providing additional genomic context.

Maintained by Benjamin Story. Last updated 5 months ago.

annotation dataimport genetics snp software singlecell alignment curl bzip2 xz-utils zlib cpp

22.5 match 1 stars 4.48 score 9 scripts

skranz

gtree:gtree basic functionality to model and solve games

gtree basic functionality to model and solve games

Maintained by Sebastian Kranz. Last updated 4 years ago.

economic-experiments economics gambit game-theory nash-equilibrium

26.4 match 18 stars 3.79 score 23 scripts 1 dependents

bioc

oposSOM:Comprehensive analysis of transcriptome data

This package translates microarray expression data into metadata of reduced dimension. It provides various sample-centered and group-centered visualizations, sample similarity analyses and functional enrichment analyses. The underlying SOM algorithm combines feature clustering, multidimensional scaling and dimension reduction, along with strong visualization capabilities. It enables extraction and description of functional expression modules inherent in the data.

Maintained by Henry Loeffler-Wirth. Last updated 5 months ago.

geneexpression differentialexpression genesetenrichment datarepresentation visualization cpp

22.3 match 4.48 score 7 scripts

moviedo5

fda.usc:Functional Data Analysis and Utilities for Statistical Computing

Routines for exploratory and descriptive analysis of functional data such as depth measurements, atypical curves detection, regression models, supervised classification, unsupervised classification and functional analysis of variance.

Maintained by Manuel Oviedo de la Fuente. Last updated 4 months ago.

functional-data-analysis fortran

10.2 match 12 stars 9.72 score 560 scripts 22 dependents

paobranco

UBL:An Implementation of Re-Sampling Approaches to Utility-Based Learning for Both Classification and Regression Tasks

Provides a set of functions that can be used to obtain better predictive performance on cost-sensitive and cost/benefits tasks (for both regression and classification). This includes re-sampling approaches that modify the original data set biasing it towards the user preferences.

Maintained by Paula Branco. Last updated 3 months ago.

fortran

15.4 match 33 stars 6.39 score 165 scripts 1 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 25 days ago.

sequencematching alignment sequencing genetics dataimport datarepresentation infrastructure bioconductor-package core-package

5.5 match 61 stars 17.83 score 8.6k scripts 1.2k dependents

edsandorf

spdesign:Designing Stated Preference Experiments

Contemporary software commonly used to design stated preference experiments are expensive and the code is closed source. This is a free software package with an easy to use interface to make flexible stated preference experimental designs using state-of-the-art methods. For an overview of stated choice experimental design theory, see e.g., Rose, J. M. & Bliemer, M. C. J. (2014) in Hess S. & Daly. A. <doi:10.4337/9781781003152>. The package website can be accessed at <https://spdesign.edsandorf.me>. We acknowledge funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant INSPiRE (Grant agreement ID: 793163).

Maintained by Erlend Dancke Sandorf. Last updated 5 months ago.

20.6 match 4.60 score 20 scripts

mrc-ide

moz.utils:Utility functions

Utility functions, for useful utilitarian uses.

Maintained by Oli Stevens. Last updated 2 months ago.

41.9 match 2.26 score 18 scripts

daroczig

logger:A Lightweight, Modern and Flexible Logging Utility

Inspired by the the 'futile.logger' R package and 'logging' Python module, this utility provides a flexible and extensible way of formatting and delivering log messages with low overhead.

Maintained by Gergely Daróczi. Last updated 2 months ago.

5.5 match 298 stars 16.88 score 1.5k scripts 98 dependents

insightsengineering

teal.logger:Logging Setup for the 'teal' Family of Packages

Utilizing the 'logger' framework to record events within a package, specific to 'teal' family of packages. Supports logging namespaces, hierarchical logging, various log destinations, vectorization, and more.

Maintained by Dawid Kaledkowski. Last updated 1 months ago.

logging nest utilities

10.5 match 5 stars 8.24 score 3 scripts 8 dependents

jhelvy

logitr:Logit Models w/Preference & WTP Space Utility Parameterizations

Fast estimation of multinomial (MNL) and mixed logit (MXL) models in R. Models can be estimated using "Preference" space or "Willingness-to-pay" (WTP) space utility parameterizations. Weighted models can also be estimated. An option is available to run a parallelized multistart optimization loop with random starting points in each iteration, which is useful for non-convex problems like MXL models or models with WTP space utility parameterizations. The main optimization loop uses the 'nloptr' package to minimize the negative log-likelihood function. Additional functions are available for computing and comparing WTP from both preference space and WTP space models and for predicting expected choices and choice probabilities for sets of alternatives based on an estimated model. Mixed logit models can include uncorrelated or correlated heterogeneity covariances and are estimated using maximum simulated likelihood based on the algorithms in Train (2009) <doi:10.1017/CBO9780511805271>. More details can be found in Helveston (2023) <doi:10.18637/jss.v105.i10>.

Maintained by John Helveston. Last updated 5 months ago.

log-likelihood logit logit-model mixed-logit mlogit multinomial-regression mxl mxl-models preference-space preferences willingness-to-pay wtp

9.3 match 54 stars 9.10 score 119 scripts 1 dependents

s3alfisc

JuliaConnectoR.utils:Utility Functions for the JuliaConnectoR

Utility functions for the JuliaConnectoR package for developers and users. Helps users of R packages that link R and Julia via JuliaConnectoR to install Julia and Julia dependencies, to connect R and Julia, to set the number of threads Julia uses from within R and to set a Julia seed from R. Helps developers to set up a github actions workflow to run both R and Julia.

Maintained by Alexander Fischer. Last updated 3 years ago.

41.3 match 2 stars 2.00 score 6 scripts

shajoezhu

DEploid.utils:'DEploid' Data Analysis and Results Interpretation

'DEploid' (Zhu et.al. 2018 <doi:10.1093/bioinformatics/btx530>) is designed for deconvoluting mixed genomes with unknown proportions. Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting. This package provides R functions to support data analysis and results interpretation.

Maintained by Joe Zhu. Last updated 3 months ago.

zlib cpp

37.5 match 2.18 score 1 dependents

r-forge

mlogit:Multinomial Logit Models

Maximum Likelihood estimation of random utility discrete choice models, as described in Kenneth Train (2009) Discrete Choice Methods with Simulations <doi:10.1017/CBO9780511805271>.

Maintained by Yves Croissant. Last updated 5 years ago.

8.2 match 9.81 score 1.2k scripts 14 dependents

kwb-r

sema.berlin.utils:Utillity Functions Used in sema.berlin Packages

This package provides utility functions that are used in sema.berlin.* packages.

Maintained by Hauke Sonnenberg. Last updated 3 years ago.

project-sema-berlin-2

36.8 match 2.18 score 1 dependents

yihui

animation:A Gallery of Animations in Statistics and Utilities to Create Animations

Provides functions for animations in statistics, covering topics in probability theory, mathematical statistics, multivariate statistics, non-parametric statistics, sampling survey, linear models, time series, computational statistics, data mining and machine learning. These functions may be helpful in teaching statistics and data analysis. Also provided in this package are a series of functions to save animations to various formats, e.g. Flash, 'GIF', HTML pages, 'PDF' and videos. 'PDF' animations can be inserted into 'Sweave' / 'knitr' easily.

Maintained by Yihui Xie. Last updated 2 years ago.

animation statistical-computing statistical-graphics statistics

6.5 match 208 stars 12.08 score 2.5k scripts 29 dependents

bioc

iSEE:Interactive SummarizedExperiment Explorer

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

Maintained by Kevin Rue-Albrecht. Last updated 12 days ago.

cellbasedassays clustering dimensionreduction featureextraction geneexpression gui immunooncology shinyapps singlecell transcription transcriptomics visualization dimension-reduction feature-extraction gene-expression hacktoberfest human-cell-atlas shiny single-cell

6.0 match 225 stars 12.86 score 380 scripts 9 dependents

rstudio

keras3:R Interface to 'Keras'

Interface to 'Keras' <https://keras.io>, a high-level neural networks API. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both CPU and GPU devices.

Maintained by Tomasz Kalinowski. Last updated 1 days ago.

5.7 match 845 stars 13.60 score 264 scripts 2 dependents

brockk

trialr:Clinical Trial Designs in 'rstan'

A collection of clinical trial designs and methods, implemented in 'rstan' and R, including: the Continual Reassessment Method by O'Quigley et al. (1990) <doi:10.2307/2531628>; EffTox by Thall & Cook (2004) <doi:10.1111/j.0006-341X.2004.00218.x>; the two-parameter logistic method of Neuenschwander, Branson & Sponer (2008) <doi:10.1002/sim.3230>; and the Augmented Binary method by Wason & Seaman (2013) <doi:10.1002/sim.5867>; and more. We provide functions to aid model-fitting and analysis. The 'rstan' implementations may also serve as a cookbook to anyone looking to extend or embellish these models. We hope that this package encourages the use of Bayesian methods in clinical trials. There is a preponderance of early phase trial designs because this is where Bayesian methods are used most. If there is a method you would like implemented, please get in touch.

Maintained by Kristian Brock. Last updated 1 years ago.

cpp

8.9 match 41 stars 8.55 score 106 scripts 3 dependents

matloff

regtools:Regression and Classification Tools

Tools for linear, nonlinear and nonparametric regression and classification. Novel graphical methods for assessment of parametric models using nonparametric methods. One vs. All and All vs. All multiclass classification, optional class probabilities adjustment. Nonparametric regression (k-NN) for general dimension, local-linear option. Nonlinear regression with Eickert-White method for dealing with heteroscedasticity. Utilities for converting time series to rectangular form. Utilities for conversion between factors and indicator variables. Some code related to "Statistical Regression and Classification: from Linear Models to Machine Learning", N. Matloff, 2017, CRC, ISBN 9781498710916.

Maintained by Norm Matloff. Last updated 2 months ago.

8.0 match 127 stars 9.39 score 48 scripts 3 dependents

polkas

pacs:Supplementary Tools for R Packages Developers

Supplementary utils for CRAN maintainers and R packages developers. Validating the library, packages and lock files. Exploring a complexity of a specific package like evaluating its size in bytes with all dependencies. The shiny app complexity could be explored too. Assessing the life duration of a specific package version. Checking a CRAN package check page status for any errors and warnings. Retrieving a DESCRIPTION or NAMESPACE file for any package version. Comparing DESCRIPTION or NAMESPACE files between different package versions. Getting a list of all releases for a specific package. The Bioconductor is partly supported.

Maintained by Maciej Nasinski. Last updated 6 months ago.

bioconductor dependencies library lifeduration renv shiny tools utils

13.2 match 25 stars 5.70 score 8 scripts

projectmosaic

mosaicData:Project MOSAIC Data Sets

Data sets from Project MOSAIC (<http://www.mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.

Maintained by Randall Pruim. Last updated 1 years ago.

9.0 match 6 stars 8.33 score 632 scripts 8 dependents

pletschm

aldvmm:Adjusted Limited Dependent Variable Mixture Models

The goal of the package 'aldvmm' is to fit adjusted limited dependent variable mixture models of health state utilities. Adjusted limited dependent variable mixture models are finite mixtures of normal distributions with an accumulation of density mass at the limits, and a gap between 100% quality of life and the next smaller utility value. The package 'aldvmm' uses the likelihood and expected value functions proposed by Hernandez Alava and Wailoo (2015) <doi:10.1177/1536867X1501500307> using normal component distributions and a multinomial logit model of probabilities of component membership.

Maintained by Mark Pletscher. Last updated 1 years ago.

clinical-trials cost-effectiveness eq5d finite-mixture health-economics hta hui limited-dependent-variable mapping mixture-model patient-reported-outcomes quality-of-life utilities

17.0 match 5 stars 4.40 score 2 scripts

bioc

GenomeInfoDb:Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

Maintained by Hervé Pagès. Last updated 2 months ago.

genetics datarepresentation annotation genomeannotation bioconductor-package core-package

4.5 match 32 stars 16.46 score 1.3k scripts 1.7k dependents

gmgeorg

LambertW:Probabilistic Models to Analyze and Gaussianize Heavy-Tailed, Skewed Data

Lambert W x F distributions are a generalized framework to analyze skewed, heavy-tailed data. It is based on an input/output system, where the output random variable (RV) Y is a non-linearly transformed version of an input RV X ~ F with similar properties as X, but slightly skewed (heavy-tailed). The transformed RV Y has a Lambert W x F distribution. This package contains functions to model and analyze skewed, heavy-tailed data the Lambert Way: simulate random samples, estimate parameters, compute quantiles, and plot/ print results nicely. The most useful function is 'Gaussianize', which works similarly to 'scale', but actually makes the data Gaussian. A do-it-yourself toolkit allows users to define their own Lambert W x 'MyFavoriteDistribution' and use it in their analysis right away.

Maintained by Georg M. Goerg. Last updated 1 years ago.

gaussianize gaussianize-data heavy-tailed heavy-tailed-distributions leptokurtosis normal-distribution normalization skewed-data statistics cpp

8.9 match 10 stars 8.17 score 78 scripts 13 dependents

bioc

biovizBase:Basic graphic utilities for visualization of genomic data.

The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.

Maintained by Michael Lawrence. Last updated 5 months ago.

infrastructure visualization preprocessing

9.0 match 8.04 score 273 scripts 75 dependents

gavinsimpson

permute:Functions for Generating Restricted Permutations of Data

A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.

Maintained by Gavin L. Simpson. Last updated 7 months ago.

permutation restricted-permutations

5.4 match 23 stars 13.28 score 538 scripts 488 dependents

bioc

ensembldb:Utilities to create and use Ensembl-based annotation databases

The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.

Maintained by Johannes Rainer. Last updated 5 months ago.

genetics annotationdata sequencing coverage annotation bioconductor bioconductor-packages ensembl

5.1 match 35 stars 14.08 score 892 scripts 108 dependents

r-lib

askpass:Password Entry Utilities for R, Git, and SSH

Cross-platform utilities for prompting the user for credentials or a passphrase, for example to authenticate with a server or read a protected key. Includes native programs for MacOS and Windows, hence no 'tcltk' is required. Password entry can be invoked in two different ways: directly from R via the askpass() function, or indirectly as password-entry back-end for 'ssh-agent' or 'git-credential' via the SSH_ASKPASS and GIT_ASKPASS environment variables. Thereby the user can be prompted for credentials or a passphrase if needed when R calls out to git or ssh.

Maintained by Jeroen Ooms. Last updated 6 months ago.

5.4 match 84 stars 12.90 score 71 scripts 5.1k dependents

mrc-ide

naomi.utils:Utility Functions For Naomi Datasets

This package contains utility functions for creating and manipulating datasets for the Naomi model and related projects.

Maintained by Jeffrey Eaton. Last updated 12 months ago.

41.2 match 1 stars 1.64 score 11 scripts

matloff

qeML:Quick and Easy Machine Learning Tools

The letters 'qe' in the package title stand for "quick and easy," alluding to the convenience goal of the package. We bring together a variety of machine learning (ML) tools from standard R packages, providing wrappers with a simple, convenient, and uniform interface.

Maintained by Norm Matloff. Last updated 27 days ago.

8.0 match 41 stars 8.41 score 48 scripts 1 dependents

cran

GE:General Equilibrium Modeling

Some tools for developing general equilibrium models and some general equilibrium models. These models can be used for teaching economic theory and are built by the methods of new structural economics (see LI Wu, 2019, ISBN: 9787521804225, General Equilibrium and Structural Dynamics: Perspectives of New Structural Economics. Beijing: Economic Science Press). The model form and mathematical methods can be traced back to J. von Neumann (1945, A Model of General Economic Equilibrium. The Review of Economic Studies, 13. pp. 1-9), J. G. Kemeny, O. Morgenstern and G. L. Thompson (1956, A Generalization of the von Neumann Model of an Expanding Economy, Econometrica, 24, pp. 115-135) et al. By the way, J. G. Kemeny is a co-inventor of the computer language BASIC.

Maintained by Wu LI. Last updated 2 months ago.

25.5 match 1 stars 2.64 score

r-forge

Matrix:Sparse and Dense Matrix Classes and Methods

A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.

Maintained by Martin Maechler. Last updated 8 days ago.

openblas

3.8 match 1 stars 17.23 score 33k scripts 12k dependents

henrikbengtsson

startup:Friendly R Startup Configuration

Adds support for R startup configuration via '.Renviron.d' and '.Rprofile.d' directories in addition to '.Renviron' and '.Rprofile' files. This makes it possible to keep private / secret environment variables separate from other environment variables. It also makes it easier to share specific startup settings by simply copying a file to a directory.

Maintained by Henrik Bengtsson. Last updated 3 months ago.

configuration environment-variables startup utility

10.0 match 166 stars 6.54 score 16 scripts

rstudio

leaflet:Create Interactive Web Maps with the JavaScript 'Leaflet' Library

Create and customize interactive maps using the 'Leaflet' JavaScript library and the 'htmlwidgets' package. These maps can be used directly from the R console, from 'RStudio', in Shiny applications and R Markdown documents.

Maintained by Joe Cheng. Last updated 14 days ago.

gis leaflet-map spatial

3.8 match 821 stars 17.20 score 39k scripts 178 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.

6.1 match 11 stars 10.58 score 872 scripts 76 dependents

bioc

SingleMoleculeFootprinting:Analysis tools for Single Molecule Footprinting (SMF) data

SingleMoleculeFootprinting provides functions to analyze Single Molecule Footprinting (SMF) data. Following the workflow exemplified in its vignette, the user will be able to perform basic data analysis of SMF data with minimal coding effort. Starting from an aligned bam file, we show how to perform quality controls over sequencing libraries, extract methylation information at the single molecule level accounting for the two possible kind of SMF experiments (single enzyme or double enzyme), classify single molecules based on their patterns of molecular occupancy, plot SMF information at a given genomic location.

Maintained by Guido Barzaghi. Last updated 29 days ago.

dnamethylation coverage nucleosomepositioning datarepresentation epigenetics methylseq qualitycontrol sequencing

10.1 match 2 stars 6.43 score 27 scripts

rvlenth

emmeans:Estimated Marginal Means, aka Least-Squares Means

Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays. Least-squares means are discussed, and the term "estimated marginal means" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.

Maintained by Russell V. Lenth. Last updated 4 days ago.

3.3 match 377 stars 19.19 score 13k scripts 187 dependents

deepayan

lattice:Trellis Graphics for R

A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements. See ?Lattice for an introduction.

Maintained by Deepayan Sarkar. Last updated 11 months ago.

3.7 match 68 stars 17.33 score 27k scripts 13k dependents

r-forge

Rmpfr:Interface R to MPFR - Multiple Precision Floating-Point Reliable

Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental ("special") functions. To this end, the package interfaces to the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library which itself is based on the 'GMP' (GNU Multiple Precision) Library.

Maintained by Martin Maechler. Last updated 4 months ago.

mpfr4 gmp

5.6 match 11.30 score 316 scripts 141 dependents

bioc

DropletUtils:Utilities for Handling Single-Cell Droplet Data

Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.

Maintained by Jonathan Griffiths. Last updated 3 months ago.

immunooncology singlecell sequencing rnaseq geneexpression transcriptomics dataimport coverage zlib cpp

6.2 match 10.08 score 2.7k scripts 9 dependents

shikokuchuo

nanonext:NNG (Nanomsg Next Gen) Lightweight Messaging Library

R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is a socket library for reliable, high-performance messaging over in-process, IPC, TCP, WebSocket and secure TLS transports. Implements 'Scalability Protocols', a standard for common communications patterns including publish/subscribe, request/reply and service discovery. As its own threaded concurrency framework, provides a toolkit for asynchronous programming and distributed computing. Intuitive 'aio' objects resolve automatically when asynchronous operations complete, and synchronisation primitives allow R to wait upon events signalled by concurrent threads.

Maintained by Charlie Gao. Last updated 3 days ago.

concurrency https ipc-message messaging-library nng rpc socket-communication synchronization-primitives tcp-protocol websocket mbedtls

6.4 match 60 stars 9.81 score 28 scripts 9 dependents

bioc

GWASTools:Tools for Genome Wide Association Studies

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.

Maintained by Stephanie M. Gogarten. Last updated 5 months ago.

snp geneticvariability qualitycontrol microarray

5.9 match 17 stars 10.50 score 396 scripts 5 dependents

lwheinsberg

dbGaPCheckup:dbGaP Checkup

Contains functions that check for formatting of the Subject Phenotype data set and data dictionary as specified by the National Center for Biotechnology Information (NCBI) Database of Genotypes and Phenotypes (dbGaP) <https://www.ncbi.nlm.nih.gov/gap/docs/submissionguide/>.

Maintained by Lacey W. Heinsberg. Last updated 1 years ago.

12.6 match 4 stars 4.86 score 18 scripts

ddalthorp

GenEst:Generalized Mortality Estimator

Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.

Maintained by Daniel Dalthorp. Last updated 2 years ago.

cpp

7.7 match 7 stars 7.81 score 55 scripts 2 dependents

neurodata

lolR:Linear Optimal Low-Rank Projection

Supervised learning techniques designed for the situation when the dimensionality exceeds the sample size have a tendency to overfit as the dimensionality of the data increases. To remedy this High dimensionality; low sample size (HDLSS) situation, we attempt to learn a lower-dimensional representation of the data before learning a classifier. That is, we project the data to a situation where the dimensionality is more manageable, and then are able to better apply standard classification or clustering techniques since we will have fewer dimensions to overfit. A number of previous works have focused on how to strategically reduce dimensionality in the unsupervised case, yet in the supervised HDLSS regime, few works have attempted to devise dimensionality reduction techniques that leverage the labels associated with the data. In this package and the associated manuscript Vogelstein et al. (2017) <arXiv:1709.01233>, we provide several methods for feature extraction, some utilizing labels and some not, along with easily extensible utilities to simplify cross-validative efforts to identify the best feature extraction method. Additionally, we include a series of adaptable benchmark simulations to serve as a standard for future investigative efforts into supervised HDLSS. Finally, we produce a comprehensive comparison of the included algorithms across a range of benchmark simulations and real data applications.

Maintained by Eric Bridgeford. Last updated 4 years ago.

8.2 match 20 stars 7.28 score 80 scripts

nicchr

cheapr:Simple Functions to Save Time and Memory

Fast and memory-efficient (or 'cheap') tools to facilitate efficient programming, saving time and memory. It aims to provide 'cheaper' alternatives to common base R functions, as well as some additional functions.

Maintained by Nick Christofides. Last updated 2 days ago.

cpp openmp

8.1 match 20 stars 7.27 score 73 scripts 2 dependents

bioc

MetaboCoreUtils:Core Utils for Metabolomics Data

MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound mass-to-charge ratios and masses or functions to work with chemical formulas. The package provides also a set of adduct definitions and information on some commercially available internal standard mixes commonly used in MS experiments.

Maintained by Johannes Rainer. Last updated 5 months ago.

infrastructure metabolomics massspectrometry mass-spectrometry

6.3 match 9 stars 9.40 score 58 scripts 36 dependents

bioc

TransView:Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

This package provides efficient tools to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.

Maintained by Julius Muller. Last updated 2 months ago.

immunooncology dnamethylation geneexpression transcription microarray sequencing chipseq rnaseq methylseq dataimport visualization clustering multiplecomparison curl bzip2 xz-utils zlib

22.5 match 2.60 score

stufield

gitr:A Lightweight API for 'Git'

A light-weight, dependency-free, application programming interface (API) to access system-level 'Git' commands from within 'R'. Contains wrappers and defaults for common data science workflows as well as 'Zsh' <https://github.com/ohmyzsh/ohmyzsh> plugin aliases. A generalized API syntax is also available. A system installation of 'Git' <https://git-scm.com/downloads> is required.

Maintained by Stu Field. Last updated 1 months ago.

git zsh

12.5 match 1 stars 4.45 score 14 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-grids h3 spatial-indexing

6.6 match 67 stars 8.39 score 205 scripts 4 dependents

hongooi73

glmnetUtils:Utilities for 'Glmnet'

Provides a formula interface for the 'glmnet' package for elasticnet regression, a method for cross-validating the alpha parameter, and other quality-of-life tools.

Maintained by Hong Ooi. Last updated 2 years ago.

cross-validation glmnet lasso regression-models

6.0 match 65 stars 9.17 score 339 scripts 5 dependents

wanchanglin

mt:Metabolomics Data Analysis Toolbox

Functions for metabolomics data analysis: data preprocessing, orthogonal signal correction, PCA analysis, PCA-DA analysis, PLS-DA analysis, classification, feature selection, correlation analysis, data visualisation and re-sampling strategies.

Maintained by Wanchang Lin. Last updated 1 years ago.

12.0 match 3 stars 4.57 score 50 scripts

bioc

CAGEfightR:Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.

Maintained by Malte Thodberg. Last updated 5 months ago.

software transcription coverage geneexpression generegulation peakdetection dataimport datarepresentation transcriptomics sequencing annotation genomebrowsers normalization preprocessing visualization

7.3 match 8 stars 7.46 score 67 scripts 1 dependents

stan-dev

cmdstanr:R Interface to 'CmdStan'

A lightweight interface to 'Stan' <https://mc-stan.org>. The 'CmdStanR' interface is an alternative to 'RStan' that calls the command line interface for compilation and running algorithms instead of interfacing with C++ via 'Rcpp'. This has many benefits including always being compatible with the latest version of Stan, fewer installation errors, fewer unexpected crashes in RStudio, and a more permissive license.

Maintained by Andrew Johnson. Last updated 9 months ago.

bayes bayesian markov-chain-monte-carlo maximum-likelihood mcmc stan variational-inference

4.5 match 145 stars 12.27 score 5.2k scripts 9 dependents

cran

futile.logger:A Logging Utility for R

Provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.

Maintained by Brian Lee Yung Rowe. Last updated 9 years ago.

5.9 match 9.32 score 1.7k scripts 1.2k dependents

r-lib

bit:Classes and Methods for Fast Memory-Efficient Boolean Selections

Provided are classes for boolean and skewed boolean vectors, fast boolean methods, fast unique and non-unique integer sorting, fast set operations on sorted and unsorted sets of integers, and foundations for ff (range index, compression, chunked processing).

Maintained by Michael Chirico. Last updated 7 days ago.

3.6 match 12 stars 15.15 score 131 scripts 3.2k dependents

r-lib

gargle:Utilities for Working with Google APIs

Provides utilities for working with Google APIs <https://developers.google.com/apis-explorer>. This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.

Maintained by Jennifer Bryan. Last updated 2 years ago.

authentication google

3.6 match 113 stars 14.88 score 266 scripts 192 dependents

laplacesdemonr

LaplacesDemon:Complete Environment for Bayesian Inference

Provides a complete environment for Bayesian inference using a variety of different samplers (see ?LaplacesDemon for an overview).

Maintained by Henrik Singmann. Last updated 12 months ago.

4.0 match 93 stars 13.45 score 1.8k scripts 60 dependents

insightsengineering

verdepcheck:Check Package using Various Versions of Dependencies

Derive package dependencies from DESCRIPTION file using various strategies and run "R CMD CHECK" to validate package compatibility.

Maintained by Pawel Rucki. Last updated 5 months ago.

check devtools testing utils

10.0 match 7 stars 5.36 score 1 scripts

r-forge

latticeExtra:Extra Graphical Utilities Based on Lattice

Building on the infrastructure provided by the lattice package, this package provides several new high-level functions and methods, as well as additional utilities such as panel and axis annotation functions.

Maintained by Deepayan Sarkar. Last updated 3 years ago.

5.2 match 10.18 score 2.6k scripts 233 dependents

earthyscience

solartime:Utilities Dealing with Solar Time Such as Sun Position and Time of Sunrise

Provide utilities to work with solar time, i.e. where noon is exactly when sun culminates. Provides functions for computing sun position and times of sunrise and sunset.

Maintained by Thomas Wutzler. Last updated 4 months ago.

7.3 match 8 stars 7.21 score 28 scripts 19 dependents

egeulgen

pathfindR:Enrichment Analysis Utilizing Active Subnetworks

Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein interaction information, resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment analysis utilizing active subnetworks. The main function identifies active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values. It then performs enrichment analyses on the identified subnetworks, identifying enriched terms (i.e. pathways or, more broadly, gene sets) that possibly underlie the phenotype of interest. 'pathfindR' also offers functionalities to cluster the enriched terms and identify representative terms in each cluster, to score the enriched terms per sample and to visualize analysis results. The enrichment, clustering and other methods implemented in 'pathfindR' are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR': An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.

Maintained by Ege Ulgen. Last updated 29 days ago.

active-subnetworks enrichment pathway pathway-enrichment-analysis subnetwork

5.2 match 186 stars 10.13 score 138 scripts

r-lib

pak:Another Approach to Package Installation

The goal of 'pak' is to make package installation faster and more reliable. In particular, it performs all HTTP operations in parallel, so metadata resolution and package downloads are fast. Metadata and package files are cached on the local disk as well. 'pak' has a dependency solver, so it finds version conflicts before performing the installation. This version of 'pak' supports CRAN, 'Bioconductor' and 'GitHub' packages as well.

Maintained by Gábor Csárdi. Last updated 2 days ago.

4.0 match 717 stars 13.05 score 277 scripts 17 dependents

ngreifer

cobalt:Covariate Balance Tables and Plots

Generate balance tables and plots for covariates of groups preprocessed through matching, weighting or subclassification, for example, using propensity scores. Includes integration with 'MatchIt', 'WeightIt', 'MatchThem', 'twang', 'Matching', 'optmatch', 'CBPS', 'ebal', 'cem', 'sbw', and 'designmatch' for assessing balance on the output of their preprocessing functions. Users can also specify data for balance assessment not generated through the above packages. Also included are methods for assessing balance in clustered or multiply imputed data sets or data sets with multi-category, continuous, or longitudinal treatments.

Maintained by Noah Greifer. Last updated 12 months ago.

causal-inference propensity-scores

4.0 match 75 stars 12.98 score 1.0k scripts 8 dependents

rchlumsk

RavenR:Raven Hydrological Modelling Framework R Support and Analysis

Utilities for processing input and output files associated with the Raven Hydrological Modelling Framework. Includes various plotting functions, model diagnostics, reading output files into extensible time series format, and support for writing Raven input files. The 'RavenR' package is also archived at Chlumsky et al. (2020) <doi:10.5281/zenodo.4248183>. The Raven Hydrologic Modelling Framework method can be referenced with Craig et al. (2020) <doi:10.1016/j.envsoft.2020.104728>.

Maintained by Robert Chlumsky. Last updated 4 months ago.

diagnostics hydrology modeling modelling visualization water water-resources watershed cpp

7.3 match 36 stars 7.06 score 20 scripts

bioc

alabaster.base:Save Bioconductor Objects to File

Save Bioconductor data structures into file artifacts, and load them back into memory. This is a more robust and portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Maintained by Aaron Lun. Last updated 13 days ago.

datarepresentation dataimport zlib cpp

6.0 match 3 stars 8.47 score 60 scripts 15 dependents

henrikbengtsson

port4me:Get the Same, Personal, Free 'TCP' Port over and over

An R implementation of the cross-platform, language-independent "port4me" algorithm (<https://github.com/HenrikBengtsson/port4me>), which (1) finds a free Transmission Control Protocol ('TCP') port in [1024,65535] that the user can open, (2) is designed to work in multi-user environments, (3), gives different users, different ports, (4) gives the user the same port over time with high probability, (5) gives different ports for different software tools, and (6) requires no configuration.

Maintained by Henrik Bengtsson. Last updated 1 years ago.

bash cli high-performance-computing hpc multi-tenant multi-user port pypi-package python r-language r-programming tcp utility

10.0 match 13 stars 5.11 score 5 scripts

hwborchers

pracma:Practical Numerical Math Functions

Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.

Maintained by Hans W. Borchers. Last updated 1 years ago.

4.1 match 29 stars 12.34 score 6.6k scripts 931 dependents

cwickham

munsell:Utilities for Using Munsell Colours

Provides easy access to, and manipulation of, the Munsell colours. Provides a mapping between Munsell's original notation (e.g. "5R 5/10") and hexadecimal strings suitable for use directly in R graphics. Also provides utilities to explore slices through the Munsell colour tree, to transform Munsell colours and display colour palettes.

Maintained by Charlotte Wickham. Last updated 12 months ago.

munsell-colour

3.6 match 110 stars 13.94 score 179 scripts 7.9k dependents

gabrielshimizu

AgroR:Experimental Statistics and Graphics for Agricultural Sciences

Performs the analysis of completely randomized experimental designs (CRD), randomized blocks (RBD) and Latin square (LSD), experiments in double and triple factorial scheme (in CRD and RBD), experiments in subdivided plot scheme (in CRD and RBD), subdivided and joint analysis of experiments in CRD and RBD, linear regression analysis, test for two samples. The package performs analysis of variance, ANOVA assumptions and multiple comparison test of means or regression, according to Pimentel-Gomes (2009, ISBN: 978-85-7133-055-9), nonparametric test (Conover, 1999, ISBN: 0471160687), test for two samples, joint analysis of experiments according to Ferreira (2018, ISBN: 978-85-7269-566-4) and generalized linear model (glm) for binomial and Poisson family in CRD and RBD (Carvalho, FJ (2019), <doi:10.14393/ufu.te.2019.1244>). It can also be used to obtain descriptive measures and graphics, in addition to correlations and creative graphics used in agricultural sciences (Agronomy, Zootechnics, Food Science and related areas).

Maintained by Gabriel Danilo Shimizu. Last updated 11 months ago.

16.3 match 1 stars 3.11 score 173 scripts

cran

bnlearn:Bayesian Network Structure Learning, Parameter Learning and Inference

Bayesian network structure learning, parameter learning and inference. This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC, Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete, Gaussian and conditional Gaussian networks, along with many score functions and conditional independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries, cross-validation, bootstrap and model averaging. Development snapshots with the latest bugfixes are available from <https://www.bnlearn.com/>.

Maintained by Marco Scutari. Last updated 2 months ago.

openblas

6.6 match 57 stars 7.72 score 32 dependents

rivolli

utiml:Utilities for Multi-Label Learning

Multi-label learning strategies and others procedures to support multi- label classification in R. The package provides a set of multi-label procedures such as sampling methods, transformation strategies, threshold functions, pre-processing techniques and evaluation metrics. A complete overview of the matter can be seen in Zhang, M. and Zhou, Z. (2014) <doi:10.1109/TKDE.2013.39> and Gibaja, E. and Ventura, S. (2015) A Tutorial on Multi-label Learning.

Maintained by Adriano Rivolli. Last updated 4 years ago.

7.9 match 28 stars 6.39 score 87 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 7 days ago.

7.7 match 6.53 score 138 scripts 18 dependents

wilsonfreitas

bizdays:Business Days Calculations and Utilities

Business days calculations based on a list of holidays and nonworking weekdays. Quite useful for fixed income and derivatives pricing.

Maintained by Wilson Freitas. Last updated 2 months ago.

bizdays business-days calendar holidays market-calendar

5.0 match 55 stars 9.89 score 426 scripts 3 dependents

bogind

easycsv:Load Multiple 'csv' and 'txt' Tables

Allows users to easily read multiple comma separated tables and create a data frame under the same name. Is able to read multiple comma separated tables from a local directory, a zip file or a zip file on a remote directory.

Maintained by Dror Bogin. Last updated 5 years ago.

csv-files easycsv utilities

10.0 match 4 stars 4.92 score 28 scripts 5 dependents

rickhelmus

patRoon:Workflows for Mass-Spectrometry Based Non-Target Analysis

Provides an easy-to-use interface to a mass spectrometry based non-target analysis workflow. Various (open-source) tools are combined which provide algorithms for extraction and grouping of features, extraction of MS and MS/MS data, automatic formula and compound annotation and grouping related features to components. In addition, various tools are provided for e.g. data preparation and cleanup, plotting results and automatic reporting.

Maintained by Rick Helmus. Last updated 11 days ago.

mass-spectrometry non-target cpp openjdk

7.9 match 65 stars 6.22 score 43 scripts

ropensci

rOPTRAM:Derive Soil Moisture Using the OPTRAM Algorithm

The OPtical TRapezoid Model (OPTRAM) derives soil moisture based on the linear relation between a vegetation index and Land Surface Temperature (LST). The Short Wave Infra-red (SWIR) band is used as a proxy for LST. See: Sadeghi, M. et al., 2017. <https://doi.org/10.1016/j.rse.2017.05.041> .

Maintained by Micha Silver. Last updated 1 months ago.

8.5 match 9 stars 5.73 score 6 scripts

forestgeo

fgeo.tool:Import and Manipulate 'ForestGEO' Data

To help you access, transform, analyze, and visualize 'ForestGEO' data, we developed a collection of R packages (<https://forestgeo.github.io/fgeo/>). This package, in particular, helps you to easily import, filter, and modify 'ForestGEO' data. To learn more about 'ForestGEO' visit <https://forestgeo.si.edu/>.

Maintained by Mauro Lepore. Last updated 3 years ago.

dynamics ecology fgeo forestgeo miscelaneas tools tree utils

10.0 match 2 stars 4.86 score 27 scripts 3 dependents

usepa

ctxR:Utilities for Interacting with the 'CTX' APIs

Access chemical, hazard, bioactivity, and exposure data from the Computational Toxicology and Exposure ('CTX') APIs <https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis>. 'ctxR' was developed to streamline the process of accessing the information available through the 'CTX' APIs without requiring prior knowledge of how to use APIs. Most data is also available on the CompTox Chemical Dashboard ('CCD') <https://comptox.epa.gov/dashboard/> and other resources found at the EPA Computational Toxicology and Exposure Online Resources <https://www.epa.gov/comptox-tools>.

Maintained by Paul Kruse. Last updated 2 months ago.

ccte comptox ord

6.0 match 10 stars 8.02 score 13 scripts 1 dependents

bioc

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.

infrastructure dataimport gui thirdpartyclient core-package u24ca289073

3.5 match 17 stars 13.89 score 2.7k scripts 102 dependents

bioc

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. Pagès. Last updated 4 months ago.

genetics infrastructure annotation sequencing genomeannotation bioconductor-package core-package

3.1 match 26 stars 15.34 score 5.3k scripts 339 dependents

hrbrmstr

hrbrthemes:Additional Themes, Theme Components and Utilities for 'ggplot2'

A compilation of extra 'ggplot2' themes, scales and utilities, including a spell check function for plot label fields and an overall emphasis on typography. A copy of the 'Google' font 'Roboto Condensed' is also included.

Maintained by Bob Rudis. Last updated 3 days ago.

data-visualization datavisualization ggplot-extension ggplot2 ggplot2-scales ggplot2-themes visualization

3.4 match 1.3k stars 13.92 score 13k scripts 15 dependents

stevenvb12

patternize:Quantification of Color Pattern Variation

Quantification of variation in organismal color patterns as obtained from image data. Patternize defines homology between pattern positions across images either through fixed landmarks or image registration. Pattern identification is performed by categorizing the distribution of colors using RGB thresholds or image segmentation.

Maintained by Steven Van Belleghem. Last updated 9 months ago.

9.6 match 31 stars 4.97 score 30 scripts

bioc

AnVIL:Bioconductor on the AnVIL compute environment

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides end-user and developer functionality. For the end-user, AnVIL provides fast binary package installation, utitlities for working with Terra / AnVIL table and data resources, and convenient functions for file movement to and from Google cloud storage. For developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls, and Dockstore RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R.

Maintained by Marcel Ramos. Last updated 24 days ago.

infrastructure

5.4 match 8.80 score 250 scripts 10 dependents

andrewljackson

SIBER:Stable Isotope Bayesian Ellipses in R

Fits bi-variate ellipses to stable isotope data using Bayesian inference with the aim being to describe and compare their isotopic niche.

Maintained by Andrew Jackson. Last updated 10 months ago.

community-ecology ecology niche-modelling stable-isotopes jags cpp

5.2 match 36 stars 9.13 score 187 scripts 1 dependents

brodieg

fansi:ANSI Control Sequence Aware String Functions

Counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.

Maintained by Brodie Gaslam. Last updated 10 months ago.

string-manipulation

3.3 match 54 stars 14.18 score 136 scripts 11k dependents

kharchenkolab

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.

cpp

7.3 match 12 stars 6.44 score 36 scripts 9 dependents

marvels2031

PWEALL:Design and Monitoring of Survival Trials Accounting for Complex Situations

Calculates various functions needed for design and monitoring survival trials accounting for complex situations such as delayed treatment effect, treatment crossover, non-uniform accrual, and different censoring distributions between groups. The event time distribution is assumed to be piecewise exponential (PWE) distribution and the entry time is assumed to be piecewise uniform distribution. As compared with Version 1.2.1, two more types of hybrid crossover are added. A bug is corrected in the function "pwecx" that calculates the crossover-adjusted survival, distribution, density, hazard and cumulative hazard functions. Also, to generate the crossover-adjusted event time random variable, a more efficient algorithm is used and the output includes crossover indicators.

Maintained by Xiaodong Luo. Last updated 2 years ago.

fortran

19.1 match 2.42 score 44 scripts 2 dependents

statistikat

simPop:Simulation of Complex Synthetic Data Information

Tools and methods to simulate populations for surveys based on auxiliary data. The tools include model-based methods, calibration and combinatorial optimization algorithms, see Templ, Kowarik and Meindl (2017) <doi:10.18637/jss.v079.i10>) and Templ (2017) <doi:10.1007/978-3-319-50272-4>. The package was developed with support of the International Household Survey Network, DFID Trust Fund TF011722 and funds from the World bank.

Maintained by Matthias Templ. Last updated 4 months ago.

cpp

7.0 match 31 stars 6.51 score 104 scripts

projectmosaic

mosaic:Project MOSAIC Statistics and Mathematics Teaching Utilities

Data sets and utilities from Project MOSAIC (<http://www.mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.

Maintained by Randall Pruim. Last updated 1 years ago.

3.4 match 93 stars 13.32 score 7.2k scripts 7 dependents

bioc

BiocBaseUtils:General utility functions for developing Bioconductor packages

The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem.

Maintained by Marcel Ramos. Last updated 5 months ago.

software infrastructure bioconductor-package core-package

5.2 match 4 stars 8.78 score 3 scripts 158 dependents

r-lib

later:Utilities for Scheduling Functions to Execute Later with Event Loops

Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied. The functions are scheduled in an event loop.

Maintained by Winston Chang. Last updated 1 months ago.

cpp

2.9 match 143 stars 15.86 score 234 scripts 2.6k dependents

azure

AzureContainers:Interface to 'Container Instances', 'Docker Registry' and 'Kubernetes' in 'Azure'

An interface to container functionality in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/product-categories/containers/>. Manage 'Azure Container Instance' (ACI), 'Azure Container Registry' (ACR) and 'Azure Kubernetes Service' (AKS) resources, push and pull images, and deploy services. On the client side, lightweight shells to the 'docker', 'docker-compose', 'kubectl' and 'helm' commandline tools are provided. Part of the 'AzureR' family of packages.

Maintained by Hong Ooi. Last updated 2 years ago.

azure-container-instances azure-container-registry azure-kubernetes-service azure-sdk-r containers kubernetes

7.0 match 25 stars 6.49 score 57 scripts

assaforon

cir:Centered Isotonic Regression and Dose-Response Utilities

Isotonic regression (IR) and its improvement: centered isotonic regression (CIR). CIR is recommended in particular with small samples. Also, interval estimates for both, and additional utilities such as plotting dose-response data. For dev version and change history, see GitHub assaforon/cir.

Maintained by Assaf P. Oron. Last updated 1 months ago.

10.1 match 4.45 score 19 scripts 1 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.

eeg eeg-analysis eeg-data eeg-signals eeg-signals-processing openblas cpp openmp

6.9 match 106 stars 6.54 score 82 scripts

dnychka

fields:Tools for Spatial Data

For curve, surface and function fitting with an emphasis on splines, spatial data, geostatistics, and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding the source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development of this package was supported in part by the National Science Foundation Grant 1417857, the National Center for Atmospheric Research, and Colorado School of Mines. See the Fields URL for a vignette on using this package and some background on spatial statistics.

Maintained by Douglas Nychka. Last updated 9 months ago.

fortran

3.6 match 15 stars 12.60 score 7.7k scripts 295 dependents

insightsengineering

tern:Create Common TLGs Used in Clinical Trials

Table, Listings, and Graphs (TLG) library for common outputs used in clinical trials.

Maintained by Joe Zhu. Last updated 2 months ago.

clinical-trials graphs listings nest outputs tables

3.5 match 79 stars 12.62 score 186 scripts 9 dependents

usepa

tcplfit2:A Concentration-Response Modeling Utility

The tcplfit2 R package performs basic concentration-response curve fitting. The original tcplFit() function in the tcpl R package performed basic concentration-response curvefitting to 3 models. With tcplfit2, the core tcpl concentration-response functionality has been expanded to process diverse high-throughput screen (HTS) data generated at the US Environmental Protection Agency, including targeted ToxCast, high-throughput transcriptomics (HTTr) and high-throughput phenotypic profiling (HTPP). tcplfit2 can be used independently to support analysis for diverse chemical screening efforts.

Maintained by Jason Brown. Last updated 13 days ago.

ccte comptox ord

6.1 match 6 stars 7.11 score 24 scripts 1 dependents

mstrimas

colorist:Coloring Wildlife Distributions in Space-Time

Color and visualize wildlife distributions in space-time using raster data. In addition to enabling display of sequential change in distributions through the use of small multiples, 'colorist' provides functions for extracting several features of interest from a sequence of distributions and for visualizing those features using HCL (hue-chroma-luminance) color palettes. Resulting maps allow for "fair" visual comparison of intensity values (e.g., occurrence, abundance, or density) across space and time and can be used to address questions about where, when, and how consistently a species, group, or individual is likely to be found.

Maintained by Matthew Strimas-Mackey. Last updated 11 months ago.

7.8 match 14 stars 5.60 score 19 scripts

fmichonneau

phylobase:Base Package for Phylogenetic Structures and Comparative Data

Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.

Maintained by Francois Michonneau. Last updated 1 years ago.

phylogenetics cpp

3.9 match 18 stars 11.14 score 394 scripts 18 dependents

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.

2.3 match 127 stars 18.63 score 35k scripts 1.3k dependents

decisionpatterns

operator.tools:Utilities for Working with R's Operators

Provides a collection of utilities that allow programming with R's operators. Routines allow classifying operators, translating to and from an operator and its underlying function, and inverting some operators (e.g. comparison operators), etc. All methods can be extended to custom infix operators.

Maintained by Christopher Brown. Last updated 7 years ago.

5.9 match 4 stars 7.26 score 23 scripts 81 dependents

jinghuazhao

gap:Genetic Analysis Package

As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. <doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).

Maintained by Jing Hua Zhao. Last updated 17 days ago.

genetics imputation lmm fortran

3.6 match 12 stars 11.88 score 448 scripts 16 dependents

emf-creaf

meteoland:Landscape Meteorology Tools

Functions to estimate weather variables at any position of a landscape [De Caceres et al. (2018) <doi:10.1016/j.envsoft.2018.08.003>].

Maintained by Miquel De Cáceres. Last updated 2 months ago.

cpp

5.4 match 10 stars 7.95 score 92 scripts 2 dependents

mclements

rstpm2:Smooth Survival Models, Including Generalized Survival Models

R implementation of generalized survival models (GSMs), smooth accelerated failure time (AFT) models and Markov multi-state models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth <doi:10.1177/0962280216664760>. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects <doi:10.1002/sim.7451>, and copulas. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0(t)=exp(-exp(eta_0(t))) is modelled for natural splines for eta_0, and the time-dependent cumulative acceleration factor eta(t,x)=\int_0^t exp(eta_1(u,x)) du for log acceleration factor eta_1(u,x). The Markov multi-state models allow for a range of models with smooth transitions to predict transition probabilities, length of stay, utilities and costs, with differences, ratios and standardisation.

Maintained by Mark Clements. Last updated 5 months ago.

fortran openblas cpp

3.9 match 28 stars 11.01 score 137 scripts 50 dependents

jacolien

plotfunctions:Various Functions to Facilitate Visualization of Data and Analysis

When analyzing data, plots are a helpful tool for visualizing data and interpreting statistical models. This package provides a set of simple tools for building plots incrementally, starting with an empty plot region, and adding bars, data points, regression lines, error bars, gradient legends, density distributions in the margins, and even pictures. The package builds further on R graphics by simply combining functions and settings in order to reduce the amount of code to produce for the user. As a result, the package does not use formula input or special syntax, but can be used in combination with default R plot functions. Note: Most of the functions were part of the package 'itsadug', which is now split in two packages: 1. the package 'itsadug', which contains the core functions for visualizing and evaluating nonlinear regression models, and 2. the package 'plotfunctions', which contains more general plot functions.

Maintained by Jacolien van Rij. Last updated 5 years ago.

9.0 match 4.73 score 94 scripts 7 dependents

r-spatial

sf:Simple Features for R

Support for simple feature access, a standardized way to encode and analyze spatial vector data. Binds to 'GDAL' <doi: 10.5281/zenodo.5884351> for reading and writing data, to 'GEOS' <doi: 10.5281/zenodo.11396894> for geometrical operations, and to 'PROJ' <doi: 10.5281/zenodo.5884394> for projection conversions and datum transformations. Uses by default the 's2' package for geometry operations on geodetic (long/lat degree) coordinates.

Maintained by Edzer Pebesma. Last updated 17 days ago.

gdal geos proj spatial cpp

1.9 match 1.4k stars 22.42 score 117k scripts 1.2k dependents

r-dbi

DBI:R Database Interface

A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.

Maintained by Kirill Müller. Last updated 3 months ago.

database interface

2.0 match 302 stars 20.88 score 19k scripts 2.9k dependents

braverock

PortfolioAnalytics:Portfolio Analysis, Including Numerical Methods for Optimization of Portfolios

Portfolio optimization and analysis routines and graphics.

Maintained by Brian G. Peterson. Last updated 3 months ago.

3.6 match 81 stars 11.49 score 626 scripts 2 dependents

fvafrcu

fritools:Utilities for the Forest Research Institute of the State Baden-Wuerttemberg

Miscellaneous utilities, tools and helper functions for finding and searching files on disk, searching for and removing R objects from the workspace. Does not import or depend on any third party package, but on core R only (i.e. it may depend on packages with priority 'base').

Maintained by Andreas Dominik Cullmann. Last updated 28 days ago.

7.0 match 5.98 score 4 scripts 6 dependents

jimbrig

jimstools:Tools for R

What the package does (one paragraph).

Maintained by Jimmy Briggs. Last updated 3 years ago.

functions personal utility

13.9 match 2 stars 3.00 score 2 scripts

bioboot

bio3d:Biological Structure Analysis

Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.

Maintained by Barry Grant. Last updated 5 months ago.

zlib cpp

4.9 match 5 stars 8.49 score 1.4k scripts 10 dependents

jaredhuling

personalized:Estimation and Validation Methods for Subgroup Identification and Personalized Medicine

Provides functions for fitting and validation of models for subgroup identification and personalized medicine / precision medicine under the general subgroup identification framework of Chen et al. (2017) <doi:10.1111/biom.12676>. This package is intended for use for both randomized controlled trials and observational studies and is described in detail in Huling and Yu (2021) <doi:10.18637/jss.v098.i05>.

Maintained by Jared Huling. Last updated 3 years ago.

causal-inference heterogeneity-of-treatment-effect individualized-treatment-rules personalized-medicine precision-medicine subgroup-identification treatment-effects treatment-scoring

5.6 match 32 stars 7.38 score 125 scripts 1 dependents

hosseinazari

StatRank:Statistical Rank Aggregation: Inference, Evaluation, and Visualization

A set of methods to implement Generalized Method of Moments and Maximal Likelihood methods for Random Utility Models. These methods are meant to provide inference on rank comparison data. These methods accept full, partial, and pairwise rankings, and provides methods to break down full or partial rankings into their pairwise components. Please see Generalized Method-of-Moments for Rank Aggregation from NIPS 2013 for a description of some of our methods.

Maintained by Hossein Azari Soufiani. Last updated 10 years ago.

12.7 match 3.24 score 58 scripts 2 dependents

mclements

biostat3:Utility Functions, Datasets and Extended Examples for Survival Analysis

Utility functions, datasets and extended examples for survival analysis. This extends a range of other packages, some simple wrappers for time-to-event analyses, datasets, and extensive examples in HTML with R scripts. The package also supports the course Biostatistics III entitled "Survival analysis for epidemiologists in R".

Maintained by Mark Clements. Last updated 2 months ago.

8.7 match 6 stars 4.73 score 153 scripts

t-kalinowski

keras:R Interface to 'Keras'

Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.

Maintained by Tomasz Kalinowski. Last updated 11 months ago.

3.8 match 10.93 score 10k scripts 55 dependents

rstudio

rmarkdown:Dynamic Documents for R

Convert R Markdown documents into a variety of formats.

Maintained by Yihui Xie. Last updated 4 months ago.

literate-programming markdown pandoc rmarkdown

1.9 match 2.9k stars 21.79 score 14k scripts 3.7k dependents

yanlinlin82

ggvenn:Draw Venn Diagram by 'ggplot2'

An easy-to-use way to draw pretty venn diagram by 'ggplot2'.

Maintained by Linlin Yan. Last updated 1 months ago.

easy-to-use ggplot2 venn-diagram

3.6 match 170 stars 11.34 score 1.8k scripts 8 dependents

hubverse-org

hubUtils:Core 'hubverse' Utilities

Core set of low-level utilities common across the 'hubverse'. Used to interact with 'hubverse' schema, Hub configuration files and model outputs and designed to be primarily used internally by other 'hubverse' packages. See Reich et al. (2022) <doi:10.2105/AJPH.2022.306831> for an overview of Collaborative Hubs.

Maintained by Anna Krystalli. Last updated 5 days ago.

hubverse

5.6 match 6 stars 7.22 score 49 scripts 7 dependents

enricoschumann

textutils:Utilities for Handling Strings and Text

Utilities for handling character vectors that store human-readable text (either plain or with markup, such as HTML or LaTeX). The package provides, in particular, functions that help with the preparation of plain-text reports, e.g. for expanding and aligning strings that form the lines of such reports. The package also provides generic functions for transforming R objects to HTML and to plain text.

Maintained by Enrico Schumann. Last updated 2 months ago.

html5 string-manipulation

5.5 match 11 stars 7.37 score 47 scripts 12 dependents

renozao

rngtools:Utility Functions for Working with Random Number Generators

Provides a set of functions for working with Random Number Generators (RNGs). In particular, a generic S4 framework is defined for getting/setting the current RNG, or RNG data that are embedded into objects for reproducibility. Notably, convenient default methods greatly facilitate the way current RNG settings can be changed.

Maintained by Renaud Gaujoux. Last updated 3 years ago.

4.7 match 6 stars 8.65 score 85 scripts 216 dependents

rdinnager

slimr:Create, Run and Post-Process 'SLiM' Population Genetics Forward Simulations

Lets you write 'SLiM' scripts (population genomics simulation) using your favourite R IDE, using a syntax as close as possible to the original 'SLiM' language. It offer many tools to manipulate those scripts, as well as run them in the 'SLiM' software from R, as well as capture and post-process their output, after or even during a simulation.

Maintained by Russell Dinnage. Last updated 4 months ago.

8.6 match 8 stars 4.70 score 42 scripts

swihart

rmutil:Utilities for Nonlinear Regression and Repeated Measurements Models

A toolkit of functions for nonlinear regression and repeated measurements not to be used by itself but called by other Lindsey packages such as 'gnlm', 'stable', 'growth', 'repeated', and 'event' (available at <https://www.commanster.eu/rcode.html>).

Maintained by Bruce Swihart. Last updated 2 years ago.

fortran

4.8 match 1 stars 8.35 score 358 scripts 70 dependents

bioc

GenomicRanges:Representation and manipulation of genomic intervals

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.

Maintained by Hervé Pagès. Last updated 4 months ago.

genetics infrastructure datarepresentation sequencing annotation genomeannotation coverage bioconductor-package core-package

2.3 match 44 stars 17.75 score 13k scripts 1.3k dependents

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 1 days ago.

fortran

2.3 match 210 stars 17.61 score 17k scripts 750 dependents

r-arcgis

arcgisutils:ArcGIS Utility Functions

Developer oriented utility functions designed to be used as the building blocks of R packages that work with ArcGIS Location Services. It provides functionality for authorization, Esri JSON construction and parsing, as well as other utilities pertaining to geometry and Esri type conversions. To support 'ArcGIS Pro' users, authorization can be done via 'arcgisbinding'. Installation instructions for 'arcgisbinding' can be found at <https://r.esri.com/r-bridge-site/docs/installation.html>.

Maintained by Josiah Parry. Last updated 1 months ago.

rust cargo

6.1 match 16 stars 6.50 score 20 scripts 5 dependents

brockk

escalation:A Modular Approach to Dose-Finding Clinical Trials

Methods for working with dose-finding clinical trials. We provide implementations of many dose-finding clinical trial designs, including the continual reassessment method (CRM) by O'Quigley et al. (1990) <doi:10.2307/2531628>, the toxicity probability interval (TPI) design by Ji et al. (2007) <doi:10.1177/1740774507079442>, the modified TPI (mTPI) design by Ji et al. (2010) <doi:10.1177/1740774510382799>, the Bayesian optimal interval design (BOIN) by Liu & Yuan (2015) <doi:10.1111/rssc.12089>, EffTox by Thall & Cook (2004) <doi:10.1111/j.0006-341X.2004.00218.x>; the design of Wages & Tait (2015) <doi:10.1080/10543406.2014.920873>, and the 3+3 described by Korn et al. (1994) <doi:10.1002/sim.4780131802>. All designs are implemented with a common interface. We also offer optional additional classes to tailor the behaviour of all designs, including avoiding skipping doses, stopping after n patients have been treated at the recommended dose, stopping when a toxicity condition is met, or demanding that n patients are treated before stopping is allowed. By daisy-chaining together these classes using the pipe operator from 'magrittr', it is simple to tailor the behaviour of a dose-finding design so it behaves how the trialist wants. Having provided a flexible interface for specifying designs, we then provide functions to run simulations and calculate dose-paths for future cohorts of patients.

Maintained by Kristian Brock. Last updated 2 months ago.

5.0 match 15 stars 7.91 score 67 scripts

hojsgaard

gRbase:A Package for Graphical Modelling in R

The 'gRbase' package provides graphical modelling features used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements graph algorithms including (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralization, (iii) triangulation, (iv) creation of junction tree. 'gRbase' facilitates array operations, 'gRbase' implements functions for testing for conditional independence. 'gRbase' illustrates how hierarchical log-linear models may be implemented and describes concept of graphical meta data. The facilities of the package are documented in the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>) and in the paper by Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>). Please see 'citation("gRbase")' for citation details.

Maintained by Søren Højsgaard. Last updated 4 months ago.

openblas cpp

4.3 match 3 stars 9.24 score 241 scripts 20 dependents

bioc

TrajectoryUtils:Single-Cell Trajectory Analysis Utilities

Implements low-level utilities for single-cell trajectory analysis, primarily intended for re-use inside higher-level packages. Include a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime inference results.

Maintained by Aaron Lun. Last updated 5 months ago.

geneexpression singlecell

6.6 match 5.91 score 16 scripts 9 dependents

r-prof

procmaps:Portable Address Space Mapping

Portable '/proc/self/maps' as a data frame. Determine which library or other region is mapped to a specific address of a process. -- R packages can contain native code, compiled to shared libraries at build or installation time. When loaded, each shared library occupies a portion of the address space of the main process. When only a machine instruction pointer is available (e.g. from a backtrace during error inspection or profiling), the address space map determines which library this instruction pointer corresponds to.

Maintained by Kirill Müller. Last updated 2 months ago.

system-utility cpp

7.5 match 3 stars 5.18 score 3 scripts 1 dependents

r-quantities

units:Measurement Units for R Vectors

Support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. Compatible with the POSIXct, Date and difftime classes. Uses the UNIDATA udunits library and unit database for unit compatibility checking and conversion. Documentation about 'units' is provided in the paper by Pebesma, Mailund & Hiebert (2016, <doi:10.32614/RJ-2016-061>), included in this package as a vignette; see 'citation("units")' for details.

Maintained by Edzer Pebesma. Last updated 5 days ago.

udunits cpp

2.3 match 181 stars 17.28 score 3.3k scripts 1.2k dependents

bioc

mia:Microbiome analysis

mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.

Maintained by Tuomas Borman. Last updated 4 days ago.

microbiome software dataimport analysis bioconductor

3.4 match 52 stars 11.50 score 316 scripts 5 dependents

neonscience

neonUtilities:Utilities for Working with NEON Data

NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org> or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.

Maintained by Claire Lunch. Last updated 1 months ago.

3.6 match 57 stars 10.66 score 944 scripts 15 dependents

ropensci

bowerbird:Keep a Collection of Sparkly Data Resources

Tools to get and maintain a data repository from third-party data providers.

Maintained by Ben Raymond. Last updated 6 days ago.

ropensci antarctic southern ocean data environmental satellite climate peer-reviewed

5.4 match 50 stars 7.16 score 16 scripts 1 dependents

spsanderson

tidyAML:Automatic Machine Learning with 'tidymodels'

The goal of this package will be to provide a simple interface for automatic machine learning that fits the 'tidymodels' framework. The intention is to work for regression and classification problems with a simple verb framework.

Maintained by Steven Sanderson. Last updated 11 months ago.

automatic-machine-learning automl classification machine-learning parsnip r-language r-programming regression tidy tidymodels tidyverse

5.6 match 68 stars 6.87 score 36 scripts 1 dependents