R-universe search: exports:info

daattali

shinyjs:Easily Improve the User Experience of Your Shiny Apps in Seconds

Perform common useful JavaScript operations in Shiny apps that will greatly improve your apps without having to know any JavaScript. Examples include: hiding an element, disabling an input, resetting an input back to its original value, delaying code execution by a few seconds, and many more useful functions for both the end user and the developer. 'shinyjs' can also be used to easily call your own custom JavaScript functions from R.

Maintained by Dean Attali. Last updated 7 months ago.

javascript shiny shiny-r

740 stars 17.28 score 8.9k scripts 400 dependents

mhahsler

arules:Mining Association Rules and Frequent Itemsets

Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). Also provides C implementations of the association mining algorithms Apriori and Eclat. Hahsler, Gruen and Hornik (2005) <doi:10.18637/jss.v014.i15>.

Maintained by Michael Hahsler. Last updated 2 months ago.

arules association-rules frequent-itemsets

194 stars 13.99 score 3.3k scripts 28 dependents

bioc

SeqArray:Data management of large-scale whole-genome sequence variant calls using GDS files

Data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.

Maintained by Xiuwen Zheng. Last updated 5 days ago.

infrastructure datarepresentation sequencing genetics bioinformatics gds-format snp snv wes wgs cpp

45 stars 12.11 score 1.1k scripts 9 dependents

bioc

VariantAnnotation:Annotation of Genetic Variants

Annotate variants, compute amino acid coding changes, predict coding outcomes.

Maintained by Bioconductor Package Maintainer. Last updated 3 months ago.

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

11.39 score 1.9k scripts 152 dependents

gdemin

expss:Tables, Labels and Some Useful Functions from Spreadsheets and 'SPSS' Statistics

Package computes and displays tables with support for 'SPSS'-style labels, multiple and nested banners, weights, multiple-response variables and significance testing. There are facilities for nice output of tables in 'knitr', 'Shiny', '*.xlsx' files, R and 'Jupyter' notebooks. Methods for labelled variables add value labels support to base R functions and to some functions from other packages. Additionally, the package brings popular data transformation functions from 'SPSS' Statistics and 'Excel': 'RECODE', 'COUNT', 'COUNTIF', 'VLOOKUP' and etc. These functions are very useful for data processing in marketing research surveys. Package intended to help people to move data processing from 'Excel' and 'SPSS' to R.

Maintained by Gregory Demin. Last updated 12 months ago.

excel labels labels-support msexcel pivot-tables recode spss spss-statistics tables variable-labels vlookup

84 stars 11.00 score 1.8k scripts 4 dependents

r-lib

log4r:A Fast and Lightweight Logging System for R, Based on 'log4j'

The log4r package is meant to provide a fast, lightweight, object-oriented approach to logging in R based on the widely-emulated 'log4j' system and etymology.

Maintained by Aaron Jacobs. Last updated 5 months ago.

logging

95 stars 10.81 score 217 scripts 16 dependents

ropensci

rerddap:General Purpose Client for 'ERDDAP™' Servers

General purpose R client for 'ERDDAP™' servers. Includes functions to search for 'datasets', get summary information on 'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format. 'ERDDAP™' information: <https://upwell.pfeg.noaa.gov/erddap/information.html>.

Maintained by Roy Mendelssohn. Last updated 8 days ago.

earth science climate precipitation temperature storm buoy noaa api-client erddap noaa-data

41 stars 10.43 score 376 scripts 5 dependents

r-forge

CHNOSZ:Thermodynamic Calculations and Diagrams for Geochemistry

An integrated set of tools for thermodynamic calculations in aqueous geochemistry and geobiochemistry. Functions are provided for writing balanced reactions to form species from user-selected basis species and for calculating the standard molal properties of species and reactions, including the standard Gibbs energy and equilibrium constant. Calculations of the non-equilibrium chemical affinity and equilibrium chemical activity of species can be portrayed on diagrams as a function of temperature, pressure, or activity of basis species; in two dimensions, this gives a maximum affinity or predominance diagram. The diagrams have formatted chemical formulas and axis labels, and water stability limits can be added to Eh-pH, oxygen fugacity- temperature, and other diagrams with a redox variable. The package has been developed to handle common calculations in aqueous geochemistry, such as solubility due to complexation of metal ions, mineral buffers of redox or pH, and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ also implements a group additivity algorithm for the standard thermodynamic properties of proteins.

Maintained by Jeffrey Dick. Last updated 20 days ago.

fortran

9.46 score 238 scripts 4 dependents

cmmr

rbiom:Read/Write, Analyze, and Visualize 'BIOM' Data

A toolkit for working with Biological Observation Matrix ('BIOM') files. Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and beta diversity (including 'UniFrac'). Summarize counts by taxonomic level. Subset based on metadata. Generate visualizations and statistical analyses. CPU intensive operations are coded in C for speed.

Maintained by Daniel P. Smith. Last updated 10 days ago.

15 stars 9.07 score 117 scripts 6 dependents

ropensci

elastic:General Purpose Interface to 'Elasticsearch'

Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java' Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' API (<https://www.elastic.co/elasticsearch/>), including functions for setting connection details to 'Elasticsearch' instances, loading bulk data, searching for documents with both 'HTTP' query variables and 'JSON' based body requests. In addition, 'elastic' provides functions for interacting with API's for 'indices', documents, nodes, clusters, an interface to the cat API, and more.

Maintained by Scott Chamberlain. Last updated 2 years ago.

database elasticsearch http api search nosql java json documents data-science database-wrapper etl

247 stars 8.98 score 151 scripts 1 dependents

bioc

ChIPpeakAnno:Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

The package encompasses a range of functions for identifying the closest gene, exon, miRNA, or custom features—such as highly conserved elements and user-supplied transcription factor binding sites. Additionally, users can retrieve sequences around the peaks and obtain enriched Gene Ontology (GO) or Pathway terms. In version 2.0.5 and beyond, new functionalities have been introduced. These include features for identifying peaks associated with bi-directional promoters along with summary statistics (peaksNearBDP), summarizing motif occurrences in peaks (summarizePatternInPeaks), and associating additional identifiers with annotated peaks or enrichedGO (addGeneIDs). The package integrates with various other packages such as biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and stat to enhance its analytical capabilities.

Maintained by Jianhong Ou. Last updated 3 months ago.

annotation chipseq chipchip

8.75 score 584 scripts 6 dependents

bioc

Voyager:From geospatial to spatial omics

SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. Bivariate methods include Lee's L and cross variogram. Multivariate methods include MULTISPATI PCA and multivariate local Geary's C recently developed by Anselin. The Voyager package also implements plotting functions to plot SFE data and ESDA results.

Maintained by Lambda Moses. Last updated 3 months ago.

geneexpression spatial transcriptomics visualization bioconductor eda esda exploratory-data-analysis omics spatial-statistics spatial-transcriptomics

88 stars 8.71 score 173 scripts

syncrosim

rsyncrosim:The R Interface to 'SyncroSim'

'SyncroSim' is a generalized framework for managing scenario-based datasets (<https://syncrosim.com/>). 'rsyncrosim' provides an interface to 'SyncroSim'. Simulation models can be added to 'SyncroSim' in order to transform these datasets, taking advantage of general features such as defining scenarios of model inputs, running Monte Carlo simulations, and summarizing model outputs. 'rsyncrosim' requires 'SyncroSim' 2.3.5 or higher (API documentation: <https://docs.syncrosim.com/>).

Maintained by Katie Birchard. Last updated 21 days ago.

9 stars 7.09 score 189 scripts

r-lidar

lasR:Fast and Pipeable Airborne LiDAR Data Tools

Fast and pipeable airborne lidar processing tools. Read/write 'las' and 'laz' files, computation of metrics in area based approach, point filtering, normalization, individual tree segmentation and other manipulations in a powerful and versatile processing chain.

Maintained by Jean-Romain Roussel. Last updated 6 hours ago.

gdal cpp openmp

19 stars 6.76 score 26 scripts

oliverehmer

act:Aligned Corpus Toolkit

The Aligned Corpus Toolkit (act) is designed for linguists that work with time aligned transcription data. It offers functions to import and export various annotation file formats ('ELAN' .eaf, 'EXMARaLDA .exb and 'Praat' .TextGrid files), create print transcripts in the style of conversation analysis, search transcripts (span searches across multiple annotations, search in normalized annotations, make concordances etc.), export and re-import search results (.csv and 'Excel' .xlsx format), create cuts for the search results (print transcripts, audio/video cuts using 'FFmpeg' and video sub titles in 'Subrib title' .srt format), modify the data in a corpus (search/replace, delete, filter etc.), interact with 'Praat' using 'Praat'-scripts, and exchange data with the 'rPraat' package. The package is itself written in R and may be expanded by other users.

Maintained by Oliver Ehmer. Last updated 2 years ago.

4 stars 6.65 score 184 scripts

thothorn

modeltools:Tools and Classes for Statistical Models

A collection of tools to deal with statistical models. The functionality is experimental and the user interface is likely to change in the future. The documentation is rather terse, but packages `coin' and `party' have some working examples. However, if you find the implemented ideas interesting we would be very interested in a discussion of this proposal. Contributions are more than welcome!

Maintained by Torsten Hothorn. Last updated 5 years ago.

6.56 score 84 scripts 254 dependents

jacolien

itsadug:Interpreting Time Series and Autocorrelated Data Using GAMMs

GAMM (Generalized Additive Mixed Modeling; Lin & Zhang, 1999) as implemented in the R package 'mgcv' (Wood, S.N., 2006; 2011) is a nonlinear regression analysis which is particularly useful for time course data such as EEG, pupil dilation, gaze data (eye tracking), and articulography recordings, but also for behavioral data such as reaction times and response data. As time course measures are sensitive to autocorrelation problems, GAMMs implements methods to reduce the autocorrelation problems. This package includes functions for the evaluation of GAMM models (e.g., model comparisons, determining regions of significance, inspection of autocorrelational structure in residuals) and interpreting of GAMMs (e.g., visualization of complex interactions, and contrasts).

Maintained by Jacolien van Rij. Last updated 3 years ago.

1 stars 6.45 score 576 scripts 2 dependents

eu-ecdc

epitweetr:Early Detection of Public Health Threats from 'Twitter' Data

It allows you to automatically monitor trends of tweets by time, place and topic aiming at detecting public health threats early through the detection of signals (e.g. an unusual increase in the number of tweets). It was designed to focus on infectious diseases, and it can be extended to all hazards or other fields of study by modifying the topics and keywords. More information is available in the 'epitweetr' peer-review publication (doi:10.2807/1560-7917.ES.2022.27.39.2200177).

Maintained by Laura Espinosa. Last updated 1 years ago.

early-warning-systems epidemic-surveillance lucene machine-learning signal-detection spark twitter

56 stars 5.98 score 86 scripts

bioc

biscuiteer:Convenience Functions for Biscuit

A test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.

Maintained by Jacob Morrison. Last updated 5 months ago.

dataimport methylseq dnamethylation

6 stars 5.98 score 16 scripts

skranz

RTutor:Interactive R problem sets with automatic testing of solutions and automatic hints

Interactive R problem sets with automatic testing of solutions and automatic hints

Maintained by Sebastian Kranz. Last updated 1 years ago.

economics learn-to-code problem-set rstudio rtutor shiny teaching

205 stars 5.83 score 111 scripts 1 dependents

cran

flexclust:Flexible Cluster Algorithms

The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability.

Maintained by Bettina Grün. Last updated 29 days ago.

3 stars 5.81 score 52 dependents

bioc

TVTB:TVTB: The VCF Tool Box

The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).

Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.

software genetics geneticvariability genomicvariation datarepresentation gui dnaseq wholegenome visualization multiplecomparison dataimport variantannotation sequencing coverage alignment sequencematching

2 stars 5.76 score 16 scripts

seankross

swirl:Learn R, in R

Use the R console as an interactive learning environment. Users receive immediate feedback as they are guided through self-paced lessons in data science and R programming.

Maintained by Sean Kross. Last updated 5 years ago.

5.57 score 1.8k scripts 1 dependents

vgherard

kgrams:Classical k-gram Language Models

Training and evaluating k-gram language models in R, supporting several probability smoothing techniques, perplexity computations, random text generation and more.

Maintained by Valerio Gherardi. Last updated 5 months ago.

language-models n-grams natural-language-processing cpp

7 stars 5.17 score 14 scripts 1 dependents

bioc

epigraHMM:Epigenomic R-based analysis with hidden Markov models

epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.

Maintained by Pedro Baldoni. Last updated 5 months ago.

chipseq atacseq dnaseseq hiddenmarkovmodel epigenetics zlib openblas cpp openmp

4.94 score 88 scripts

eddelbuettel

spdl:Easier Use of 'RcppSpdlog' Functions via Wrapper

Logging functions in 'RcppSpdlog' provide access to the logging functionality from the 'spdlog' 'C++' library. This package offers shorter convenience wrappers for the 'R' functions which match the 'C++' functions, namely via, say, 'spdl::debug()' at the debug level. The actual formatting is done by the 'fmt::format()' function from the 'fmtlib' library (that is also 'std::format()' in 'C++20' or later).

Maintained by Dirk Eddelbuettel. Last updated 10 months ago.

2 stars 4.78 score 1 scripts 6 dependents

bioc

iBBiG:Iterative Binary Biclustering of Genesets

iBBiG is a bi-clustering algorithm which is optimizes for binary data analysis. We apply it to meta-gene set analysis of large numbers of gene expression datasets. The iterative algorithm extracts groups of phenotypes from multiple studies that are associated with similar gene sets. iBBiG does not require prior knowledge of the number or scale of clusters and allows discovery of clusters with diverse sizes

Maintained by Aedin Culhane. Last updated 5 months ago.

clustering annotation genesetenrichment

4.56 score 3 scripts 2 dependents

chronosphere-info

chronosphere:Evolving Earth System Variables

The implemented functions allow the query, download, and import of remotely-stored and version-controlled data items. The inherent meta-database maps data files and import code to programming classes and allows access to these items via files deposited in public repositories. The purpose of the project is to increase reproducibility and establish version tracking of results from (paleo)environmental/ecological research.

Maintained by Adam T. Kocsis. Last updated 2 years ago.

6 stars 4.53 score 56 scripts

flr

FLSAM:An Implementation of the State-Space Assessment Model for FLR

This package provides an FLR wrapper to the SAM state-space assessment model.

Maintained by N.T. Hintzen. Last updated 4 months ago.

4 stars 4.51 score 406 scripts

setempler

miscset:Miscellaneous Tools Set

A collection of miscellaneous methods to simplify various tasks, including plotting, data.frame and matrix transformations, environment functions, regular expression methods, and string and logical operations, as well as numerical and statistical tools. Most of the methods are simple but useful wrappers of common base R functions, which extend S3 generics or provide default values for important parameters.

Maintained by Sven E. Templer. Last updated 8 years ago.

miscellaneous cpp

1 stars 4.40 score 50 scripts

bioc

BubbleTree:BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data

CNV analysis in groups of tumor samples.

Maintained by Todd Creasy. Last updated 5 months ago.

copynumbervariation software sequencing coverage

3.95 score 15 scripts

bioc

rqubic:Qualitative biclustering algorithm for expression data analysis in R

This package implements the QUBIC algorithm introduced by Li et al. for the qualitative biclustering with gene expression data.

Maintained by Jitao David Zhang. Last updated 5 months ago.

clustering

3.78 score 4 scripts 1 dependents

stan-dev

posteriordb:R functionality for posteriordb

R functionality of easy handling of the posteriordb posteriors.

Maintained by Mans Magnusson. Last updated 2 years ago.

8 stars 3.37 score 59 scripts

sens

qtlDesign:Design of QTL (Quantitative Trait Locus) Experiments

Design of QTL (quantitative trait locus) experiments involves choosing which strains to cross, the type of cross, genotyping strategies, phenotyping strategies, and the number of progeny to raise and phenotype. This package provides tools to help make such choices. Sen and others (2007) <doi:10.1007/s00335-006-0090-y>.

Maintained by Saunak Sen. Last updated 12 months ago.

1 stars 2.90 score 32 scripts

hwangq

irtQ:Unidimensional Item Response Theory Modeling

Fit unidimensional item response theory (IRT) models to a mixture of dichotomous and polytomous data, calibrate online item parameters (i.e., pretest and operational items), estimate examinees' abilities, and examine the IRT model-data fit on item-level in different ways as well as provide useful functions related to IRT analyses such as IRT model-data fit evaluation and differential item functioning analysis. The bring.flexmirt() and write.flexmirt() functions were written by modifying the read.flexmirt() function (Pritikin & Falk (2022) <doi:10.1177/0146621620929431>). The bring.bilog() and bring.parscale() functions were written by modifying the read.bilog() and read.parscale() functions, respectively (Weeks (2010) <doi:10.18637/jss.v035.i12>). The bisection() function was written by modifying the bisection() function (Howard (2017, ISBN:9780367657918)). The code of the inverse test characteristic curve scoring in the est_score() function was written by modifying the irt.eq.tse() function (González (2014) <doi:10.18637/jss.v059.i07>). In est_score() function, the code of weighted likelihood estimation method was written by referring to the Pi(), Ji(), and Ii() functions of the catR package (Magis & Barrada (2017) <doi:10.18637/jss.v076.c01>).

Maintained by Hwanggyu Lim. Last updated 7 months ago.

2 stars 2.00 score 2 scripts

chadgoymer

msgr:Extends Messages, Warnings and Errors by Adding Levels and Log Files

Provides new functions info(), warn() and error(), similar to message(), warning() and stop() respectively. However, the new functions can have a 'level' associated with them, so that when executed the global level option determines whether they are shown or not. This allows debug modes, outputting more information. The can also output all messages to a log file.

Maintained by Chad Goymer. Last updated 5 years ago.

1.70 score 1 scripts