R-universe search: bracket

bioc

MultiAssayExperiment:Software for the integration of multi-omics experiments in Bioconductor

Harmonize data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.

Maintained by Marcel Ramos. Last updated 2 months ago.

infrastructure datarepresentation bioconductor bioconductor-package genomics nci-itcr tcga u24ca289073

5.5 match 71 stars 14.94 score 670 scripts 126 dependents

tbates

umx:Structural Equation Modeling and Twin Modeling in R

Quickly create, run, and report structural equation models, and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.

Maintained by Timothy C. Bates. Last updated 7 hours ago.

behavior-genetics genetics openmx psychology sem statistics structural-equation-modeling tutorials twin-models umx

7.1 match 44 stars 9.35 score 472 scripts

bioc

Structstrings:Implementation of the dot bracket annotations with Biostrings

The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.

Maintained by Felix G.M. Ernst. Last updated 5 months ago.

dataimport datarepresentation infrastructure sequencing software alignment sequencematching bioconductor rna rna-structural-analysis rna-structure sequences structures

10.2 match 4 stars 6.46 score 3 scripts 4 dependents

csdaw

ggprism:A 'ggplot2' Extension Inspired by 'GraphPad Prism'

Provides various themes, palettes, and other functions that are used to customise ggplots to look like they were made in 'GraphPad Prism'. The 'Prism'-look is achieved with theme_prism() and scale_fill|colour_prism(), axes can be changed with custom guides like guide_prism_minor(), and significance indicators added with add_pvalue().

Maintained by Charlotte Dawson. Last updated 1 years ago.

ggplot-extension ggplot2 prism

6.2 match 175 stars 10.56 score 1.1k scripts 5 dependents

const-ae

ggsignif:Significance Brackets for 'ggplot2'

Enrich your 'ggplots' with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance (NS, *, **, ***). The package provides a single layer (geom_signif()) that takes the groups for comparison and the test (t.test(), wilcox.text() etc.) as arguments and adds the annotation to the plot.

Maintained by Constantin Ahlmann-Eltze. Last updated 8 months ago.

asterisk ggplot-extension ggplot2 significance-stars

3.8 match 601 stars 16.89 score 3.6k scripts 417 dependents

lrberge

fixest:Fast Fixed-Effects Estimations

Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial. The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://github.com/lrberge/fixest/blob/master/_DOCS/FENmlm_paper.pdf>. Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.

Maintained by Laurent Berge. Last updated 7 months ago.

cpp openmp

4.1 match 394 stars 14.69 score 3.8k scripts 26 dependents

nicolash2

ggbrace:Curly Braces for 'ggplot2'

Provides curly braces in 'ggplot2' plus matching text. stat_brace() plots braces partially in the confines of data so that the brace is set apart from it. stat_bracetext() plots corresponding text, fitting to the braces from stat_brace().

Maintained by Nicolas Huber. Last updated 1 years ago.

brace braces bracket ggplot ggplot2 graph graphs plot

11.0 match 13 stars 5.08 score 93 scripts

sportsdataverse

hoopR:Access Men's Basketball Play by Play Data

A utility to quickly obtain clean and tidy men's basketball play by play data. Provides functions to access live play by play and box score data from ESPN<https://www.espn.com> with shot locations when available. It is also a full NBA Stats API<https://www.nba.com/stats/> wrapper. It is also a scraping and aggregating interface for Ken Pomeroy's men's college basketball statistics website<https://kenpom.com>. It provides users with an active subscription the capability to scrape the website tables and analyze the data for themselves.

Maintained by Saiem Gilani. Last updated 1 years ago.

basketball college-basketball espn kenpom nba nba-analytics nba-api nba-data nba-statistics nba-stats nba-stats-api ncaa ncaa-basketball ncaa-bracket ncaa-players ncaa-ratings ncaam sportsdataverse

7.5 match 91 stars 6.93 score 261 scripts

paulnorthrop

itp:The Interpolate, Truncate, Project (ITP) Root-Finding Algorithm

Implements the Interpolate, Truncate, Project (ITP) root-finding algorithm developed by Oliveira and Takahashi (2021) <doi:10.1145/3423597>. The user provides the function, from the real numbers to the real numbers, and an interval with the property that the values of the function at its endpoints have different signs. If the function is continuous over this interval then the ITP method estimates the value at which the function is equal to zero. If the function is discontinuous then a point of discontinuity at which the function changes sign may be found. The function can be supplied using either an R function or an external pointer to a C++ function. Tuning parameters of the ITP algorithm can be set by the user. Default values are set based on arguments in Oliveira and Takahashi (2021).

Maintained by Paul J. Northrop. Last updated 10 months ago.

algorithm bracketing itp itp-method root-finding cpp

10.0 match 12 stars 5.08 score 8 scripts

enricoschumann

NMOF:Numerical Methods and Optimization in Finance

Functions, examples and data from the first and the second edition of "Numerical Methods and Optimization in Finance" by M. Gilli, D. Maringer and E. Schumann (2019, ISBN:978-0128150658). The package provides implementations of optimisation heuristics (Differential Evolution, Genetic Algorithms, Particle Swarm Optimisation, Simulated Annealing and Threshold Accepting), and other optimisation tools, such as grid search and greedy search. There are also functions for the valuation of financial instruments such as bonds and options, for portfolio selection and functions that help with stochastic simulations.

Maintained by Enrico Schumann. Last updated 3 days ago.

black-scholes differential-evolution genetic-algorithm grid-search heuristics implied-volatility local-search optimization particle-swarm-optimization simulated-annealing threshold-accepting

5.3 match 37 stars 9.27 score 101 scripts 3 dependents

cran

pBrackets:Plot Brackets

Adds different kinds of brackets to a plot, including braces, chevrons, parentheses or square brackets.

Maintained by Andreas Schulz. Last updated 4 years ago.

18.8 match 2.48 score 1 dependents

stefanedwards

lemon:Freshing Up your 'ggplot2' Plots

Functions for working with legends and axis lines of 'ggplot2', facets that repeat axis lines on all panels, and some 'knitr' extensions.

Maintained by Stefan McKinnon Edwards. Last updated 5 months ago.

axis-lines facets ggplot-extension ggplot2 knitr legend ticks visualization

3.8 match 190 stars 11.98 score 1.7k scripts 4 dependents

rudeboybert

fivethirtyeight:Data and Code Behind the Stories and Interactives at 'FiveThirtyEight'

Datasets and code published by the data journalism website 'FiveThirtyEight' available at <https://github.com/fivethirtyeight/data>. Note that while we received guidance from editors at 'FiveThirtyEight', this package is not officially published by 'FiveThirtyEight'.

Maintained by Albert Y. Kim. Last updated 2 years ago.

data-science datajournalism fivethirtyeight statistics

3.8 match 453 stars 10.98 score 1.7k scripts

matthewheun

RCLabels:Manipulate Matrix Row and Column Labels with Ease

Functions to assist manipulation of matrix row and column labels for all types of matrix mathematics where row and column labels are to be respected.

Maintained by Matthew Heun. Last updated 27 days ago.

8.5 match 1 stars 4.78 score 5 scripts 2 dependents

bstaton1

postpack:Utilities for Processing Posterior Samples Stored in 'mcmc.lists'

The aim of 'postpack' is to provide the infrastructure for a standardized workflow for 'mcmc.list' objects. These objects can be used to store output from models fitted with Bayesian inference using 'JAGS', 'WinBUGS', 'OpenBUGS', 'NIMBLE', 'Stan', or even custom MCMC algorithms. Although the 'coda' R package provides some methods for these objects, it is somewhat limited in easily performing post-processing tasks for specific nodes. Models are ever increasing in their complexity and the number of tracked nodes, and oftentimes a user may wish to summarize/diagnose sampling behavior for only a small subset of nodes at a time for a particular question or figure. Thus, many 'postpack' functions support performing tasks on a subset of nodes, where the subset is specified with regular expressions. The functions in 'postpack' streamline the extraction, summarization, and diagnostics of specific monitored nodes after model fitting. Further, because there is rarely only ever one model under consideration, 'postpack' scales efficiently to perform the same tasks on output from multiple models simultaneously, facilitating rapid assessment of model sensitivity to changes in assumptions.

Maintained by Ben Staton. Last updated 2 years ago.

5.1 match 2 stars 6.75 score 233 scripts 1 dependents

davidgohel

flextable:Functions for Tabular Reporting

Use a grammar for creating and customizing pretty tables. The following formats are supported: 'HTML', 'PDF', 'RTF', 'Microsoft Word', 'Microsoft PowerPoint' and R 'Grid Graphics'. 'R Markdown', 'Quarto' and the package 'officer' can be used to produce the result files. The syntax is the same for the user regardless of the type of output to be produced. A set of functions allows the creation, definition of cell arrangement, addition of headers or footers, formatting and definition of cell content with text and or images. The package also offers a set of high-level functions that allow tabular reporting of statistical models and the creation of complex cross tabulations.

Maintained by David Gohel. Last updated 8 days ago.

docx html5 ms-office-documents rmarkdown table

2.0 match 582 stars 17.09 score 7.3k scripts 124 dependents

teunbrand

legendry:Extended Legends and Axes for 'ggplot2'

A 'ggplot2' extension that focusses on expanding the plotter's arsenal of guides. Guides in 'ggplot2' include axes and legends. 'legendry' offers new axes and annotation options, as well as new legends and colour displays.

Maintained by Teun van den Brand. Last updated 26 days ago.

axis axis-customization ggplot-extension ggplot2 legend visualization

4.3 match 227 stars 7.83 score 29 scripts 2 dependents

kassambara

ggpubr:'ggplot2' Based Publication Ready Plots

The 'ggplot2' package is excellent and flexible for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.

Maintained by Alboukadel Kassambara. Last updated 2 years ago.

1.9 match 1.2k stars 16.68 score 65k scripts 409 dependents

adamlilith

omnibus:Helper Tools for Managing Data, Dates, Missing Values, and Text

An assortment of helper functions for managing data (e.g., rotating values in matrices by a user-defined angle, switching from row- to column-indexing), dates (e.g., intuiting year from messy date strings), handling missing values (e.g., removing elements/rows across multiple vectors or matrices if any have an NA), text (e.g., flushing reports to the console in real-time); and combining data frames with different schema (copying, filling, or concatenating columns or applying functions before combining).

Maintained by Adam B. Smith. Last updated 6 months ago.

count-decimals leap-year merge-lists missing-values rotate-matrix sampling

5.1 match 4 stars 5.83 score 54 scripts 3 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 6 months ago.

6.3 match 4.60 score 20 scripts

faosorios

fastmatrix:Fast Computation of some Matrices Useful in Statistics

Small set of functions to fast computation of some matrices and operations useful in statistics and econometrics. Currently, there are functions for efficient computation of duplication, commutation and symmetrizer matrices with minimal storage requirements. Some commonly used matrix decompositions (LU and LDL), basic matrix operations (for instance, Hadamard, Kronecker products and the Sherman-Morrison formula) and iterative solvers for linear systems are also available. In addition, the package includes a number of common statistical procedures such as the sweep operator, weighted mean and covariance matrix using an online algorithm, linear regression (using Cholesky, QR, SVD, sweep operator and conjugate gradients methods), ridge regression (with optimal selection of the ridge parameter considering several procedures), omnibus tests for univariate normality, functions to compute the multivariate skewness, kurtosis, the Mahalanobis distance (checking the positive defineteness), and the Wilson-Hilferty transformation of gamma variables. Furthermore, the package provides interfaces to C code callable by another C code from other R packages.

Maintained by Felipe Osorio. Last updated 1 years ago.

commutation-matrix jarque-bera-test ldl-factorization lu-factorization matrix-api-for-r-packages matrix-norms modified-cholesky ols-regression power-method ridge-regression sherman-morrison statistics sweep-operator symmetrizer-matrix fortran openblas

4.5 match 19 stars 6.37 score 37 scripts 11 dependents

leonawicz

tabr:Music Notation Syntax, Manipulation, Analysis and Transcription in R

Provides a music notation syntax and a collection of music programming functions for generating, manipulating, organizing, and analyzing musical information in R. Music syntax can be entered directly in character strings, for example to quickly transcribe short pieces of music. The package contains functions for directly performing various mathematical, logical and organizational operations and musical transformations on special object classes that facilitate working with music data and notation. The same music data can be organized in tidy data frames for a familiar and powerful approach to the analysis of large amounts of structured music data. Functions are available for mapping seamlessly between these formats and their representations of musical information. The package also provides an API to 'LilyPond' (<https://lilypond.org/>) for transcribing musical representations in R into tablature ("tabs") and sheet music. 'LilyPond' is open source music engraving software for generating high quality sheet music based on markup syntax. The package generates 'LilyPond' files from R code and can pass them to the 'LilyPond' command line interface to be rendered into sheet music PDF files or inserted into R markdown documents. The package offers nominal MIDI file output support in conjunction with rendering sheet music. The package can read MIDI files and attempts to structure the MIDI data to integrate as best as possible with the data structures and functionality found throughout the package.

Maintained by Matthew Leonawicz. Last updated 7 months ago.

guitar-tablature lilypond lilypond-api music-analysis music-data music-notation music-programming music-syntax music-transcription sheet-music

3.6 match 132 stars 7.87 score 94 scripts

jinkim3

kim:A Toolkit for Behavioral Scientists

A collection of functions for analyzing data typically collected or used by behavioral scientists. Examples of the functions include a function that compares groups in a factorial experimental design, a function that conducts two-way analysis of variance (ANOVA), and a function that cleans a data set generated by Qualtrics surveys. Some of the functions will require installing additional package(s). Such packages and other references are cited within the section describing the relevant functions. Many functions in this package rely heavily on these two popular R packages: Dowle et al. (2021) <https://CRAN.R-project.org/package=data.table>. Wickham et al. (2021) <https://CRAN.R-project.org/package=ggplot2>.

Maintained by Jin Kim. Last updated 1 months ago.

5.3 match 7 stars 4.62 score 3 scripts

kkholst

lava:Latent Variable Models

A general implementation of Structural Equation Models with latent variables (MLE, 2SLS, and composite likelihood estimators) with both continuous, censored, and ordinal outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>). Mixture latent variable models and non-linear latent variable models (Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>). The package also provides methods for graph exploration (d-separation, back-door criterion), simulation of general non-linear latent variable models, and estimation of influence functions for a broad range of statistical models.

Maintained by Klaus K. Holst. Last updated 3 months ago.

latent-variable-models simulation statistics structural-equation-models

1.9 match 33 stars 12.87 score 610 scripts 478 dependents

crsh

papaja:Prepare American Psychological Association Journal Articles with R Markdown

Tools to create dynamic, submission-ready manuscripts, which conform to American Psychological Association manuscript guidelines. We provide R Markdown document formats for manuscripts (PDF and Word) and revision letters (PDF). Helper functions facilitate reporting statistical analyses or create publication-ready tables and plots.

Maintained by Frederik Aust. Last updated 1 months ago.

apa apa-guidelines journal manuscript psychology reproducible-paper reproducible-research rmarkdown

2.0 match 663 stars 12.00 score 1.7k scripts 2 dependents

cran

tableMatrix:Combines 'data.table' and 'matrix' Classes

Provides two classes extending 'data.table' class. Simple 'tableList' class wraps 'data.table' and any additional structures together. More complex 'tableMatrix' class combines 'data.table' and 'matrix'. See <http://github.com/InferenceTechnologies/tableMatrix> for more information and examples.

Maintained by Petr Lenhard. Last updated 7 years ago.

8.9 match 2.70 score

ncss-tech

aqp:Algorithms for Quantitative Pedology

The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.

Maintained by Dylan Beaudette. Last updated 1 months ago.

digital-soil-mapping ncss-tech nrcs pedology pedometrics soil soil-survey usda

2.0 match 55 stars 11.90 score 1.2k scripts 2 dependents

robinhankin

hyper2:The Hyperdirichlet Distribution, Mark 2

A suite of routines for the hyperdirichlet distribution and reified Bradley-Terry; supersedes the 'hyperdirichlet' package; uses 'disordR' discipline <doi:10.48550/ARXIV.2210.03856>. To cite in publications please use Hankin 2017 <doi:10.32614/rj-2017-061>, and for Generalized Plackett-Luce likelihoods use Hankin 2024 <doi:10.18637/jss.v109.i08>.

Maintained by Robin K. S. Hankin. Last updated 3 days ago.

cpp

3.0 match 5 stars 7.91 score 38 scripts 1 dependents

biodiverse

unmarked:Models for Data from Unmarked Animals

Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.

Maintained by Ken Kellner. Last updated 12 days ago.

openblas cpp openmp

1.8 match 4 stars 13.02 score 652 scripts 12 dependents

insightsengineering

teal.modules.clinical:'teal' Modules for Standard Clinical Outputs

Provides user-friendly tools for creating and customizing clinical trial reports. By leveraging the 'teal' framework, this package provides 'teal' modules to easily create an interactive panel that allows for seamless adjustments to data presentation, thereby streamlining the creation of detailed and accurate reports.

Maintained by Dawid Kaledkowski. Last updated 1 months ago.

clinical-trials modules nest outputs shiny

2.3 match 35 stars 10.21 score 149 scripts

trinker

qdap:Bridging the Gap Between Qualitative Data and Quantitative Analysis

Automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse including frequency counts of sentence types, words, sentences, turns of talk, syllables and other assorted analysis tasks. The package provides parsing tools for preparing transcript data. Many functions enable the user to aggregate data by any number of grouping variables, providing analysis and seamless integration with other R packages that undertake higher level analysis and visualization of text. This affords the user a more efficient and targeted analysis. 'qdap' is designed for transcript analysis, however, many functions are applicable to other areas of Text Mining/ Natural Language Processing.

Maintained by Tyler Rinker. Last updated 5 years ago.

qdap quantitative-discourse-analysis text-analysis text-mining text-plotting openjdk

2.3 match 176 stars 9.61 score 1.3k scripts 3 dependents

welch-lab

rliger:Linked Inference of Genomic Experimental Relationships

Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.

Maintained by Yichen Wang. Last updated 3 months ago.

nonnegative-matrix-factorization single-cell openblas cpp

2.0 match 408 stars 10.77 score 334 scripts 1 dependents

deankoch

snapKrig:Fast Kriging and Geostatistics on Grids with Kronecker Covariance

Geostatistical modeling and kriging with gridded data using spatially separable covariance functions (Kronecker covariances). Kronecker products in these models provide shortcuts for solving large matrix problems in likelihood and conditional mean, making 'snapKrig' computationally efficient with large grids. The package supplies its own S3 grid object class, and a host of methods including plot, print, Ops, square bracket replace/assign, and more. Our computational methods are described in Koch, Lele, Lewis (2020) <doi:10.7939/r3-g6qb-bq70>.

Maintained by Dean Koch. Last updated 5 months ago.

4.2 match 5 stars 5.05 score 15 scripts

bioc

tRNA:Analyzing tRNA sequences and structures

The tRNA package allows tRNA sequences and structures to be accessed and used for subsetting. In addition, it provides visualization tools to compare feature parameters of multiple tRNA sets and correlate them to additional data. The tRNA package uses GRanges objects as inputs requiring only few additional column data sets.

Maintained by Felix GM Ernst. Last updated 5 months ago.

software visualization bioconductor sequences structures trna

3.1 match 1 stars 6.69 score 3 scripts 3 dependents

haddonm

MQMF:Modelling and Quantitative Methods in Fisheries

Complements the book "Using R for Modelling and Quantitative Methods in Fisheries" ISBN 9780367469894, published in 2021 by Chapman & Hall in their "Using R series". There are numerous functions and data-sets that are used in the book's many practical examples.

Maintained by Malcolm Haddon. Last updated 2 years ago.

ecology fisheries haddon quantitative-methods uncertainty

5.0 match 11 stars 4.14 score 25 scripts

bioc

ncRNAtools:An R toolkit for non-coding RNA

ncRNAtools provides a set of basic tools for handling and analyzing non-coding RNAs. These include tools to access the RNAcentral database and to predict and visualize the secondary structure of non-coding RNAs. The package also provides tools to read, write and interconvert the file formats most commonly used for representing such secondary structures.

Maintained by Lara Selles Vidal. Last updated 5 months ago.

functionalgenomics dataimport thirdpartyclient visualization structuralprediction

6.0 match 1 stars 3.38 score 12 scripts

bioc

dreamlet:Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

Recent advances in single cell/nucleus transcriptomic technology has enabled collection of cohort-scale datasets to study cell type specific gene expression differences associated disease state, stimulus, and genetic regulation. The scale of these data, complex study designs, and low read count per cell mean that characterizing cell type specific molecular mechanisms requires a user-frieldly, purpose-build analytical framework. We have developed the dreamlet package that applies a pseudobulk approach and fits a regression model for each gene and cell cluster to test differential expression across individuals associated with a trait of interest. Use of precision-weighted linear mixed models enables accounting for repeated measures study designs, high dimensional batch effects, and varying sequencing depth or observed cells per biosample.

Maintained by Gabriel Hoffman. Last updated 6 days ago.

rnaseq geneexpression differentialexpression batcheffect qualitycontrol regression genesetenrichment generegulation epigenetics functionalgenomics transcriptomics normalization singlecell preprocessing sequencing immunooncology software cpp

2.3 match 12 stars 8.14 score 128 scripts

bioc

DECIPHER:Tools for curating, analyzing, and manipulating biological sequences

A toolset for deciphering and managing biological sequences.

Maintained by Erik Wright. Last updated 21 days ago.

clustering genetics sequencing dataimport visualization microarray qualitycontrol qpcr alignment wholegenome microbiome immunooncology geneprediction openmp

1.7 match 10.55 score 1.1k scripts 14 dependents

trinker

qdapRegex:Regular Expression Removal, Extraction, and Replacement Tools

A collection of regular expression tools associated with the 'qdap' package that may be useful outside of the context of discourse analysis. Tools include removal/extraction/replacement of abbreviations, dates, dollar amounts, email addresses, hash tags, numbers, percentages, citations, person tags, phone numbers, times, and zip codes.

Maintained by Tyler Rinker. Last updated 9 days ago.

qdapregex regular-expression

1.9 match 50 stars 9.47 score 502 scripts 41 dependents

khankawsar

Durga:Effect Size Estimation and Visualisation

An easy-to-use yet powerful system for plotting grouped data effect sizes. Various types of effect size can be estimated, then plotted together with a representation of the original data. Select from many possible data representations (box plots, violin plots, raw data points etc.), and combine as desired. 'Durga' plots are implemented in base R, so are compatible with base R methods for combining plots, such as 'layout()'. See Khan & McLean (2023) <doi:10.1101/2023.02.06.526960>.

Maintained by Jim McLean. Last updated 3 months ago.

3.4 match 4 stars 5.20 score 5 scripts

bioc

rhdf5client:Access HDF5 content from HDF Scalable Data Service

This package provides functionality for reading data from HDF Scalable Data Service from within R. The HSDSArray function bridges from HSDS to the user via the DelayedArray interface. Bioconductor manages an open HSDS instance graciously provided by John Readey of the HDF Group.

Maintained by Vincent Carey. Last updated 5 months ago.

dataimport software infrastructure

3.6 match 4.82 score 37 scripts 2 dependents

fsolt

dotwhisker:Dot-and-Whisker Plots of Regression Results

Create quick and easy dot-and-whisker plots of regression results. It takes as input either (1) a coefficient table in standard form or (2) one (or a list of) fitted model objects (of any type that has methods implemented in the 'parameters' package). It returns 'ggplot' objects that can be further customized using tools from the 'ggplot2' package. The package also includes helper functions for tasks such as rescaling coefficients or relabeling predictor variables. See more methodological discussion of the visualization and data management methods used in this package in Kastellec and Leoni (2007) <doi:10.1017/S1537592707072209> and Gelman (2008) <doi:10.1002/sim.3107>.

Maintained by Yue Hu. Last updated 6 months ago.

graphics plot regression-models

1.7 match 60 stars 10.14 score 680 scripts

billpetti

baseballr:Acquiring and Analyzing Baseball Data

Provides numerous utilities for acquiring and analyzing baseball data from online sources such as 'Baseball Reference' <https://www.baseball-reference.com/>, 'FanGraphs' <https://www.fangraphs.com/>, and the 'MLB Stats' API <https://www.mlb.com/>.

Maintained by Saiem Gilani. Last updated 5 months ago.

baseball pitchfx sabermetrics statcast

1.9 match 380 stars 8.98 score 582 scripts

njbultman

sleeperapi:Wrapper Functions Around 'Sleeper' (Fantasy Sports) API

For those wishing to interact with the 'Sleeper' (Fantasy Sports) API (<https://docs.sleeper.com/>) without looking too much into its documentation (found at <https://docs.sleeper.com/>), this package offers wrapper functions around the available API calls to make it easier.

Maintained by Nick Bultman. Last updated 4 months ago.

3.8 match 6 stars 4.48 score 8 scripts

gpilgrim2670

SwimmeR:Data Import, Cleaning, and Conversions for Swimming Results

The goal of the 'SwimmeR' package is to provide means of acquiring, and then analyzing, data from swimming (and diving) competitions. To that end 'SwimmeR' allows results to be read in from .html sources, like 'Hy-Tek' real time results pages, '.pdf' files, 'ISL' results, 'Omega' results, and (on a development basis) '.hy3' files. Once read in, 'SwimmeR' can convert swimming times (performances) between the computationally useful format of seconds reported to the '100ths' place (e.g. 95.37), and the conventional reporting format (1:35.37) used in the swimming community. 'SwimmeR' can also score meets in a variety of formats with user defined point values, convert times between courses ('LCM', 'SCM', 'SCY') and draw single elimination brackets, as well as providing a suite of tools for working cleaning swimming data. This is a developmental package, not yet mature.

Maintained by Greg Pilgrim. Last updated 2 years ago.

3.7 match 4 stars 4.53 score 17 scripts

lrberge

stringmagic:Character String Operations and Interpolation, Magic Edition

Performs complex string operations compactly and efficiently. Supports string interpolation jointly with over 50 string operations. Also enhances regular string functions (like grep() and co). See an introduction at <https://lrberge.github.io/stringmagic/>.

Maintained by Laurent R Berge. Last updated 8 months ago.

interpolation string cpp

1.5 match 15 stars 10.56 score 37 scripts 33 dependents

gdemin

maditr:Fast Data Aggregation, Modification, and Filtering with Pipes and 'data.table'

Provides pipe-style interface for 'data.table'. Package preserves all 'data.table' features without significant impact on performance. 'let' and 'take' functions are simplified interfaces for most common data manipulation tasks. For example, you can write 'take(mtcars, mean(mpg), by = am)' for aggregation or 'let(mtcars, hp_wt = hp/wt, hp_wt_mpg = hp_wt/mpg)' for modification. Use 'take_if/let_if' for conditional aggregation/modification. Additionally there are some conveniences such as automatic 'data.frame' conversion to 'data.table'.

Maintained by Gregory Demin. Last updated 5 months ago.

data-table magrittr pipes

1.8 match 61 stars 8.98 score 248 scripts 7 dependents

insightsengineering

teal:Exploratory Web Apps for Analyzing Clinical Trials Data

A 'shiny' based interactive exploration framework for analyzing clinical trials data. 'teal' currently provides a dynamic filtering facility and different data viewers. 'teal' 'shiny' applications are built using standard 'shiny' modules.

Maintained by Dawid Kaledkowski. Last updated 1 months ago.

clinical-trials nest shiny webapp

1.2 match 206 stars 12.65 score 176 scripts 5 dependents

pecanproject

PEcAn.LPJGUESS:PEcAn Package for Integration of the LPJ-GUESS Model

This module provides functions to link LPJ-GUESS to PEcAn.

Maintained by Istem Fer. Last updated 2 hours ago.

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

2.0 match 216 stars 7.58 score 1 scripts

bwiernik

pipebind:Flexible Binding for Complex Function Evaluation with the Base R |> Pipe

Provides a simple function to bind a piped object to a placeholder symbol to enable complex function evaluation with the base R |> pipe.

Maintained by Brenton M. Wiernik. Last updated 2 years ago.

3.3 match 49 stars 4.54 score 14 scripts

sigbertklinke

exams.forge:Support for Compiling Examination Tasks using the 'exams' Package

The main aim is to further facilitate the creation of exercises based on the package 'exams' by Grün, B., and Zeileis, A. (2009) <doi:10.18637/jss.v029.i10>. Creating effective student exercises involves challenges such as creating appropriate data sets and ensuring access to intermediate values for accurate explanation of solutions. The functionality includes the generation of univariate and bivariate data including simple time series, functions for theoretical distributions and their approximation, statistical and mathematical calculations for tasks in basic statistics courses as well as general tasks such as string manipulation, LaTeX/HTML formatting and the editing of XML task files for 'Moodle'.

Maintained by Sigbert Klinke. Last updated 9 months ago.

5.5 match 2.70 score 1 scripts

bioc

flowWorkspace:Infrastructure for representing and interacting with gated and ungated cytometry data sets.

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

Maintained by Greg Finak. Last updated 25 days ago.

immunooncology flowcytometry dataimport preprocessing datarepresentation zlib openblas cpp

1.8 match 7.89 score 576 scripts 10 dependents

calvagone

campsismod:Generic Implementation of a PK/PD Model

A generic, easy-to-use and expandable implementation of a pharmacokinetic (PK) / pharmacodynamic (PD) model based on the S4 class system. This package allows the user to read/write a pharmacometric model from/to files and adapt it further on the fly in the R environment. For this purpose, this package provides an intuitive API to add, modify or delete equations, ordinary differential equations (ODE's), model parameters or compartment properties (like infusion duration or rate, bioavailability and initial values). Finally, this package also provides a useful export of the model for use with simulation packages 'rxode2' and 'mrgsolve'. This package is designed and intended to be used with package 'campsis', a PK/PD simulation platform built on top of 'rxode2' and 'mrgsolve'.

Maintained by Nicolas Luyckx. Last updated 16 hours ago.

2.0 match 5 stars 6.95 score 42 scripts 1 dependents

t-kalinowski

yasp:String Functions for Compact R Code

A collection of string functions designed for writing compact and expressive R code. 'yasp' (Yet Another String Package) is simple, fast, dependency-free, and written in pure R. The package provides: a coherent set of abbreviations for paste() from package 'base' with a variety of defaults, such as p() for "paste" and pcc() for "paste and collapse with commas"; wrap(), bracket(), and others for wrapping a string in flanking characters; unwrap() for removing pairs of characters (at any position in a string); and sentence() for cleaning whitespace around punctuation and capitalization appropriate for prose sentences.

Maintained by Tomasz Kalinowski. Last updated 6 years ago.

3.8 match 8 stars 3.60 score 4 scripts

detlew

PowerTOST:Power and Sample Size for (Bio)Equivalence Studies

Contains functions to calculate power and sample size for various study designs used in bioequivalence studies. Use known.designs() to see the designs supported. Power and sample size can be obtained based on different methods, amongst them prominently the TOST procedure (two one-sided t-tests). See README and NEWS for further information.

Maintained by Detlew Labes. Last updated 1 years ago.

1.5 match 20 stars 9.10 score 112 scripts 4 dependents

graemetlloyd

Claddis:Measuring Morphological Diversity and Evolutionary Tempo

Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees. Imports morphological data from #NEXUS (Maddison et al. (1997) <doi:10.1093/sysbio/46.4.590>) format with read_nexus_matrix(), and writes to both #NEXUS and TNT format (Goloboff et al. (2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main functions are test_rates(), which implements AIC and likelihood ratio tests for discrete character rates introduced across Lloyd et al. (2012) <doi:10.1111/j.1558-5646.2011.01460.x>, Brusatte et al. (2014) <doi:10.1016/j.cub.2014.08.034>, Close et al. (2015) <doi:10.1016/j.cub.2015.06.047>, and Lloyd (2016) <doi:10.1111/bij.12746>, and calculate_morphological_distances(), which implements multiple discrete character distance metrics from Gower (1971) <doi:10.2307/2528823>, Wills (1998) <doi:10.1006/bijl.1998.0255>, Lloyd (2016) <doi:10.1111/bij.12746>, and Hopkins and St John (2018) <doi:10.1098/rspb.2018.1784>. This also includes the GED correction from Lehmann et al. (2019) <doi:10.1111/pala.12430>. Multiple functions implement morphospace plots: plot_chronophylomorphospace() implements Sakamoto and Ruta (2012) <doi:10.1371/journal.pone.0039752>, plot_morphospace() implements Wills et al. (1994) <doi:10.1017/S009483730001263X>, plot_changes_on_tree() implements Wang and Lloyd (2016) <doi:10.1098/rspb.2016.0214>, and plot_morphospace_stack() implements Foote (1993) <doi:10.1017/S0094837300015864>. Other functions include safe_taxonomic_reduction(), which implements Wilkinson (1995) <doi:10.1093/sysbio/44.4.501>, map_dollo_changes() implements the Dollo stochastic character mapping of Tarver et al. (2018) <doi:10.1093/gbe/evy096>, and estimate_ancestral_states() implements the ancestral state options of Lloyd (2018) <doi:10.1111/pala.12380>. calculate_tree_length() and reconstruct_ancestral_states() implements the generalised algorithms from Swofford and Maddison (1992; no doi).

Maintained by Graeme T. Lloyd. Last updated 7 days ago.

1.7 match 13 stars 7.86 score 77 scripts 2 dependents

bcjaeger

table.glue:Make and Apply Customized Rounding Specifications for Tables

Translate double and integer valued data into character values formatted for tabulation in manuscripts or other types of academic reports.

Maintained by Byron Jaeger. Last updated 4 months ago.

2.3 match 7 stars 5.92 score 60 scripts

cb4ds

DGEobj:Differential Gene Expression (DGE) Analysis Results Data Object

Provides a flexible container to manage and annotate Differential Gene Expression (DGE) analysis results (Smythe et. al (2015) <doi:10.1093/nar/gkv007>). The DGEobj has data slots for row (gene), col (samples), assays (matrix n-rows by m-samples dimensions) and metadata (not keyed to row, col, or assays). A set of accessory functions to deposit, query and retrieve subsets of a data workflow has been provided. Attributes are used to capture metadata such as species and gene model, including reproducibility information such that a 3rd party can access a DGEobj history to see how each data object was created or modified. Since the DGEobj is customizable and extensible it is not limited to RNA-seq analysis types of workflows -- it can accommodate nearly any data analysis workflow that starts from a matrix of assays (rows) by samples (columns).

Maintained by Connie Brett. Last updated 2 months ago.

2.0 match 2 stars 5.60 score 33 scripts 2 dependents

leonawicz

lcars:LCARS Aesthetic for Shiny

Provides Shiny widgets and theme that support a 'Library Computer Access/Retrieval System' (LCARS) aesthetic for Shiny apps. The package also includes functions for adding a minimal LCARS theme to static 'ggplot2' graphs. More details about LCARS can be found at <https://en.wikipedia.org/wiki/LCARS>.

Maintained by Matthew Leonawicz. Last updated 7 months ago.

lcars r-shiny star-trek

2.0 match 70 stars 5.54 score 9 scripts

dsjohnson

crawl:Fit Continuous-Time Correlated Random Walk Models to Animal Movement Data

Fit continuous-time correlated random walk models with time indexed covariates to animal telemetry data. The model is fit using the Kalman-filter on a state space version of the continuous-time stochastic movement process.

Maintained by Devin S. Johnson. Last updated 6 months ago.

openblas cpp

1.8 match 19 stars 6.29 score 63 scripts 3 dependents

miyamot0

fxl:'fxl' Single Case Design Charting Package

The 'fxl' Charting package is used to prepare and design single case design figures that are typically prepared in spreadsheet software. With 'fxl', there is no need to leave the R environment to prepare these works and many of the more unique conventions in single case experimental designs can be performed without the need for physically constructing features of plots (e.g., drawing annotations across plots). Support is provided for various different plotting arrangements (e.g., multiple baseline), annotations (e.g., brackets, arrows), and output formats (e.g., svg, rasters).

Maintained by Shawn Gilroy. Last updated 3 months ago.

behavior-analysis single-case-design visual-analysis

2.0 match 8 stars 5.46 score 24 scripts

lhdjung

scrutiny:Error Detection in Science

Test published summary statistics for consistency (Brown and Heathers, 2017, <doi:10.1177/1948550616673876>; Allard, 2018, <https://aurelienallard.netlify.app/post/anaytic-grimmer-possibility-standard-deviations/>; Heathers and Brown, 2019, <https://osf.io/5vb3u/>). The package also provides infrastructure for implementing new error detection techniques.

Maintained by Lukas Jung. Last updated 6 months ago.

1.8 match 8 stars 6.22 score 38 scripts

elipousson

cliExtras:A Collection of Helper Functions for the cli package

Extends the cli package with user response prompts and stopifnot equivalents.

Maintained by Eli Pousson. Last updated 12 months ago.

cli

3.0 match 3 stars 3.56 score 2 scripts 8 dependents

jrvarma

jrvFinance:Basic Finance; NPV/IRR/Annuities/Bond-Pricing; Black Scholes

Implements the basic financial analysis functions similar to (but not identical to) what is available in most spreadsheet software. This includes finding the IRR and NPV of regularly spaced cash flows and annuities. Bond pricing and YTM calculations are included. In addition, Black Scholes option pricing and Greeks are also provided.

Maintained by Jayanth Varma. Last updated 3 years ago.

1.7 match 12 stars 5.94 score 48 scripts 1 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

2.0 match 2 stars 4.95 score 2 scripts

poissonconsulting

err:Customizable Object Sensitive Messages

Messages should provide users with readable information about R objects without flooding their console. 'cc()' concatenates vector and data frame values into a grammatically correct string using commas, an ellipsis and conjunction. 'cn()' allows the user to define a string which varies based on a count. 'co()' combines the two to produce a customizable object aware string. The package further facilitates this process by providing five 'sprintf'-like types such as '%n' for the length of an object and '%o' for its name as well as wrappers for pasting objects and issuing errors, warnings and messages.

Maintained by Joe Thorley. Last updated 3 months ago.

errors messages warnings

1.9 match 7 stars 4.80 score 50 scripts 2 dependents

nimble-dev

nimbleMacros:Macros Generating 'nimble' Code

Macros to generate 'nimble' code from a concise syntax. Included are macros for generating linear modeling code using a formula-based syntax and for building for() loops. For more details review the 'nimble' manual: <https://r-nimble.org/html_manual/cha-writing-models.html#subsec:macros>.

Maintained by Ken Kellner. Last updated 20 days ago.

1.7 match 4.98 score

hughparsonage

TeXCheckR:Parses LaTeX Documents for Errors

Checks LaTeX documents and .bib files for typing errors, such as spelling errors, incorrect quotation marks. Also provides useful functions for parsing and linting bibliography files.

Maintained by Hugh Parsonage. Last updated 1 years ago.

bibtex latex spellcheck

1.9 match 8 stars 4.44 score 23 scripts

jestonblu

RobinHood:Interface for the RobinHood.com No Commission Investing Platform

Execute API calls to the RobinHood <https://robinhood.com> investing platform. Functionality includes accessing account data and current holdings, retrieving investment statistics and quotes, placing and canceling orders, getting market trading hours, searching investments by popular tag, and interacting with watch lists.

Maintained by Joseph Blubaugh. Last updated 2 years ago.

algotrading api robinhood robinhood-api trade

1.7 match 45 stars 4.58 score 17 scripts

bioc

xenLite:Simple classes and methods for managing Xenium datasets

Define a relatively light class for managing Xenium data using Bioconductor. Address use of parquet for coordinates, SpatialExperiment for assay and sample data. Address serialization and use of cloud storage.

Maintained by Vincent Carey. Last updated 5 months ago.

infrastructure

1.7 match 1 stars 4.48 score 4 scripts

hmu-wh

ggcompare:Mean Comparison in 'ggplot2'

Add mean comparison annotations to a 'ggplot'. This package provides an easy way to indicate if two or more groups are significantly different in a 'ggplot'. Usually you do not need to specify the test method, you only need to tell stat_compare() whether you want to perform a parametric test or a nonparametric test, and stat_compare() will automatically choose the appropriate test method based on your data. For comparisons between two groups, the p-value is calculated by t-test (parametric) or Wilcoxon rank sum test (nonparametric). For comparisons among more than two groups, the p-value is calculated by One-way ANOVA (parametric) or Kruskal-Wallis test (nonparametric).

Maintained by Hao Wang. Last updated 4 months ago.

1.9 match 4 stars 3.30 score 2 scripts

hugoquene

hqmisc:Miscellaneous Convenience Functions and Dataset

Miscellaneous convenience functions and wrapper functions to convert frequencies between Hz, semitones, mel and Bark, to create a matrix of dummy columns from a factor, to determine whether x lies in range [a,b], and to add a bracketed line to an existing plot. This package also contains an example data set of a stratified sample of 80 talkers of Dutch.

Maintained by Hugo Quene. Last updated 3 years ago.

5.7 match 1.08 score 12 scripts

pik-piam

reportbrick:Reporting package for BRICK

This package contains BRICK-specific routines to report model results. The main functionality is to generate a mif-file from a given BRICK model run folder.

Maintained by Robin Hasse. Last updated 1 months ago.

1.8 match 3.48 score 2 dependents

skranz

stringtools:Tools for working with strings in R

Tools for working with strings in R

Maintained by Sebastian Kranz. Last updated 3 years ago.

1.7 match 2 stars 3.66 score 29 scripts 26 dependents

ghurault

HuraultMisc:Guillem Hurault Functions' Library

Contains various functions for data analysis, notably helpers and diagnostics for Bayesian modelling using Stan.

Maintained by Guillem Hurault. Last updated 4 months ago.

bayesian-statistics data-analysis statistical-models

1.7 match 2.95 score 18 scripts

ajc29

lorenz:Tools for Deriving Income Inequality Estimates from Grouped Income Data

Provides two methods of estimating income inequality statistics from binned income data, such as the income data provided in the Census. These methods use different interpolation techniques to infer the distribution of incomes within income bins. One method is an implementation of Jargowsky and Wheeler's mean-constrained integration over brackets (MCIB). The other method is based on a new technique, Lorenz interpolation, which estimates income inequality by constructing an interpolated Lorenz curve based on the binned income data. These methods can be used to estimate three income inequality measures: the Gini (the default measure returned), the Theil, and the Atkinson's index. Jargowsky and Wheeler (2018) <doi:10.1177/0081175018782579>.

Maintained by Andrew Carr. Last updated 5 years ago.

2.2 match 1.70 score 5 scripts

skranz

rmdtools:Tools for RMarkdown

Tools for RMarkdown

Maintained by Sebastian Kranz. Last updated 4 years ago.

2.0 match 1 stars 1.78 score 6 scripts 2 dependents

cran

Tex4exams:Generating 'Sweave' Code for 'R/exams' Questions in Mathematics

When using the R package 'exams' to write mathematics questions in 'Sweave' files, the output of a lot of R functions need to be adjusted for display in mathematical formulas. Specifically, the functions were accumulated when writing questions for the topics of the mathematics courses College Algebra, Precalculus, Calculus, Differential Equations, Introduction to Probability, and Linear Algebra. The output of the developed functions can be used in 'Sweave' files.

Maintained by Qingwen Hu. Last updated 2 years ago.

3.4 match 1.00 score

cran

podcleaner:Legacy Scottish Post Office Directories Cleaner

Attempts to clean optical character recognition (OCR) errors in legacy Scottish Post Office Directories. Further attempts to match records from trades and general directories.

Maintained by Olivier Bautheac. Last updated 3 years ago.

1.8 match 1.70 score

geobosh

lagged:Classes and Methods for Lagged Objects

Provides classes and methods for objects, whose indexing naturally starts from zero. Subsetting, indexing and mathematical operations are defined naturally between lagged objects and lagged and base R objects. Recycling is not used, except for singletons. The single bracket operator doesn't drop dimensions by default.

Maintained by Georgi N. Boshnakov. Last updated 3 years ago.

0.5 match 4.59 score 13 scripts 2 dependents

professorbeautiful

NNTbiomarker:Calculate Design Parameters for Biomarker Validation Studies

Helps a clinical trial team discuss the clinical goals of a well-defined biomarker with a diagnostic, staging, prognostic, or predictive purpose. From this discussion will come a statistical plan for a (non-randomized) validation trial. Both prospective and retrospective trials are supported. In a specific focused discussion, investigators should determine the range of "discomfort" for the NNT, number needed to treat. The meaning of the discomfort range, [NNTlower, NNTupper], is that within this range most physicians would feel discomfort either in treating or withholding treatment. A pair of NNT values bracketing that range, NNTpos and NNTneg, become the targets of the study's design. If the trial can demonstrate that a positive biomarker test yields an NNT less than NNTlower, and that a negative biomarker test yields an NNT less than NNTlower, then the biomarker may be useful for patients. A highlight of the package is visualization of a "contra-Bayes" theorem, which produces criteria for retrospective case-controls studies.

Maintained by Roger Day. Last updated 6 years ago.

0.5 match 3.65 score 15 scripts

vigou3

roger:Automated Grading of R Scripts

Tools for grading the coding style and documentation of R scripts. This is the R component of Roger the Omni Grader, an automated grading system for computer programming projects based on Unix shell scripts; see <https://gitlab.com/roger-project>. The package also provides an R interface to the shell scripts. Inspired by the lintr package.

Maintained by Vincent Goulet. Last updated 1 years ago.

1.8 match 1.00 score 5 scripts

bioc

rfaRm:An R interface to the Rfam database

rfaRm provides a client interface to the Rfam database of RNA families. Data that can be retrieved include RNA families, secondary structure images, covariance models, sequences within each family, alignments leading to the identification of a family and secondary structures in the dot-bracket format.

Maintained by Lara Selles Vidal. Last updated 5 months ago.

functionalgenomics dataimport thirdpartyclient visualization multiplesequencealignment

0.5 match 3.30 score 1 scripts

bairuzhang

INSPECTumours:IN-vivo reSPonsE Classification of Tumours

This is a shiny app used for the statistical classifying and analysing pre-clinical tumour responses.

Maintained by Bairu Zhang. Last updated 3 years ago.

1.6 match 1.00 score 3 scripts