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rhdf5 - R Interface to HDF5

This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

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infrastructuredataimportbioconductorhdf5rhdf5curlopensslcpp

17.05 score 74 stars 293 dependents 6.5k scripts 54k downloads

biomaRt - Interface to BioMart databases (i.e. Ensembl)

In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (<https://www.ensembl.org/info/data/biomart/index.html>). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintained by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.

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annotationbioconductorbiomartensembl

15.26 score 51 stars 233 dependents 18k scripts 47k downloads

scoringutils - Utilities for Scoring and Assessing Predictions

Facilitate the evaluation of forecasts in a convenient framework based on data.table. It allows user to to check their forecasts and diagnose issues, to visualise forecasts and missing data, to transform data before scoring, to handle missing forecasts, to aggregate scores, and to visualise the results of the evaluation. The package mostly focuses on the evaluation of probabilistic forecasts and allows evaluating several different forecast types and input formats. Find more information about the package in the Vignettes as well as in the accompanying paper, <doi:10.48550/arXiv.2205.07090>.

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forecast-evaluationforecasting

11.76 score 65 stars 9 dependents 475 scripts 1.9k downloads

Rhdf5lib - hdf5 library as an R package

Provides C and C++ hdf5 libraries.

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infrastructurebioconductorhdf5hdf5-library

11.75 score 7 stars 414 dependents 35 scripts 56k downloads

Rarr - A Simple and Performant Native R Reader & Writer for Zarr Arrays

The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. Its design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specification in R with minimal reliance on an external tools or libraries.

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dataimportbioconductorome-ngffome-zarron-diskout-of-memoryzarrc-blosclibzstd

11.16 score 55 stars 9 dependents 103 scripts 1.4k downloads

Rarr - A Simple and Performant Native R Reader & Writer for Zarr Arrays

The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. Its design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specification in R with minimal reliance on an external tools or libraries.

Last updated

dataimportbioconductorome-ngffome-zarron-diskout-of-memoryzarrc-blosclibzstd

11.01 score 55 stars 9 dependents 99 scripts

socialmixr - Social Mixing Matrices for Infectious Disease Modelling

Methods for sampling contact matrices from diary data for use in infectious disease modelling, as discussed in Mossong et al. (2008) <doi:10.1371/journal.pmed.0050074>.

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11.00 score 44 stars 2 dependents 409 scripts 844 downloads

rhdf5filters - HDF5 Compression Filters

Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seamless integration with rhdf5, however the compiled filters can also be used with external applications.

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infrastructuredataimportcompressionfilter-pluginhdf5

10.57 score 5 stars 294 dependents 12 scripts 51k downloads

pavo - Perceptual Analysis, Visualization and Organization of Spectral Colour Data

A cohesive framework for the spectral and spatial analysis of colour described in Maia, Eliason, Bitton, Doucet & Shawkey (2013) <doi:10.1111/2041-210X.12069> and Maia, Gruson, Endler & White (2019) <doi:10.1111/2041-210X.13174>.

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10.28 score 81 stars 2 dependents 159 scripts 1.2k downloads

epinowcast - A Bayesian Framework for Real-Time Infectious Disease Surveillance

A modular Bayesian framework for real-time infectious disease surveillance. Provides tools for nowcasting, reproduction number estimation, delay estimation, and forecasting from data subject to reporting delays, right-truncation, missing data, and incomplete ascertainment. Users can build models suited to their setting using a flexible formula interface supporting fixed effects, random effects, random walks, and time-varying parameters, with options including parametric and non-parametric delay distributions with optional modifiers (via discrete-time hazard models), renewal processes, observation models, missing data imputation, and stratified analyses with partial pooling. By jointly estimating disease dynamics and reporting patterns, our framework enables earlier and more reliable detection of trends. While designed with epidemiological applications in mind, the framework can be applied to any right-truncated time series count data.

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cmdstanreffective-reproduction-number-estimationepidemiologyinfectious-disease-surveillancenowcastingoutbreak-analysispandemic-preparednessreal-time-infectious-disease-modellingstan

9.07 score 67 stars 101 scripts

spatialdataR - Representation of Python's spatialdata in R

R interface to Python/scverse's 'spatialdata' framework for unified spatial omics data handling. Adheres to OME-NGFF standards, providing lazy, on-disk representations for multiscale images and labels (ZarrArray), as well as points and shapes (DuckDB-backed tables). Includes handling of coordinate transformation systems and spatial utilities for cropping, masking, and querying. Integrates tabular annotations as 'SingleCellExperiment's (via 'anndataR'), enabling interoperable spatial omics workflows across R and Python.

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dataimportdatarepresentationinfrastructureimmunooncologygeneexpressiontranscriptomicssinglecellspatial

8.83 score 41 stars 2 dependents 25 scripts

arrayQualityMetrics - Quality metrics report for microarray data sets

This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.

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microarrayqualitycontrolonechanneltwochannelreportwritingbioconductor

8.70 score 1 stars 1 dependents 338 scripts 1.4k downloads

fundiversity - Easy Computation of Functional Diversity Indices

Computes six functional diversity indices. These are namely, Functional Divergence (FDiv), Function Evenness (FEve), Functional Richness (FRic), Functional Richness intersections (FRic_intersect), Functional Dispersion (FDis), and Rao's entropy (Q) (reviewed in Villéger et al. 2008 <doi:10.1890/07-1206.1>). Provides efficient, modular, and parallel functions to compute functional diversity indices (Grenié & Gruson 2023 <doi:10.1111/ecog.06585>).

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biodiversitybiodiversity-indicatorsbiodiversity-informaticsfunctional-diversityfunctional-ecologyfunctional-traitfunctional-traitstraittrait-basedtraits

8.16 score 45 stars 1 dependents 53 scripts 528 downloads

lightr - Read Spectrometric Data and Metadata

Parse various reflectance/transmittance/absorbance spectra file formats to extract spectral data and metadata, as described in Gruson, White & Maia (2019) <doi:10.21105/joss.01857>. Among other formats, it can import files from 'Avantes' <https://www.avantes.com/>, 'CRAIC' <https://www.microspectra.com/>, and 'OceanOptics'/'OceanInsight' <https://www.oceanoptics.com/> brands.

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file-importreproducibilityreproducible-researchreproducible-sciencespectral-dataspectroscopy

8.14 score 15 stars 3 dependents 19 scripts 778 downloads

lightr - Read Spectrometric Data and Metadata

Parse various reflectance/transmittance/absorbance spectra file formats to extract spectral data and metadata, as described in Gruson, White & Maia (2019) <doi:10.21105/joss.01857>. Among other formats, it can import files from 'Avantes' <https://www.avantes.com/>, 'CRAIC' <https://www.microspectra.com/>, and 'OceanOptics'/'OceanInsight' <https://www.oceanoptics.com/> brands.

Last updated

file-importreproducibilityreproducible-researchreproducible-sciencespectral-dataspectroscopy

8.14 score 15 stars 3 dependents 19 scripts 778 downloads

DEXSeq - Inference of differential exon usage in RNA-Seq

The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

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immunooncologysequencingrnaseqdifferentialexpressionalternativesplicingdifferentialsplicinggeneexpressionvisualization

8.11 score 7 dependents 508 scripts 4.0k downloads

grumpy - Read 'NumPy' '.npy' and '.npz' Files

Lightweight way to read 'NumPy' '.npy' and '.npz' files in R. All data types supported by 'NumPy', with all sizes (converted internally to R native size), both C and 'Fortran' order, and any shape, up to an arbitrary number of dimensions, are supported.

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data-formatdata-importinteroperabilitynpy-filesnpz-filesnumpy-filesquarto

7.91 score 9 stars 10 dependents 7 scripts 888 downloads

linelist - Tagging and Validating Epidemiological Data

Provides tools to help storing and handling case line list data. The 'linelist' class adds a tagging system to classical 'data.frame' objects to identify key epidemiological data such as dates of symptom onset, epidemiological case definition, age, gender or disease outcome. Once tagged, these variables can be seamlessly used in downstream analyses, making data pipelines more robust and reliable.

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datadata-structuresepidemiologyepiverseoutbreakssdg-3structured-data

7.88 score 11 stars 2 dependents 83 scripts 648 downloads

ZarrArray - Bring Zarr datasets in R as DelayedArray objects

The ZarrArray package leverages the Rarr package to bring Zarr datasets in R as DelayedArray objects. The main class in the package is the ZarrArray class. A ZarrArray object is an array-like object that represents a Zarr dataset in R. ZarrArray objects are DelayedArray derivatives and therefore support all operations (delayed or block-processed) supported by DelayedArray objects.

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infrastructuredatarepresentationdataimportbioconductor-packagecore-packageu24ca289073

7.48 score 5 stars 8 dependents 13 scripts

SpatialData.plot - SpatialData visualization

Visualization suit for 'spatialdataR'. Current functionality includes handling of multiscale 'images', visualizing 'labels', 'points', and 'shapes'. For the latter, POINT, POLYGON, and MULTIPOLYGON geometries are supported. For all but 'images', there is support to pass information from annotation 'tables' as aesthetics (e.g., 'colData' or 'assay' data).

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spatialsinglecellvisualizationinfrastructureimmunooncologygeneexpressiontranscriptomics

5.83 score 8 stars 28 scripts

contactdata - Social Contact Matrices for 177 Countries

Data package for the supplementary data in Prem et al. (2017) <doi:10.1371/journal.pcbi.1005697> and Prem et al. <doi:10.1371/journal.pcbi.1009098>. Provides easy access to contact data for 177 countries, for use in epidemiological, demographic or social sciences research.

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demographicsepidemiologysocial-sciences

5.56 score 11 stars 22 scripts 460 downloads

contactdata - Social Contact Matrices for 177 Countries

Data package for the supplementary data in Prem et al. (2017) <doi:10.1371/journal.pcbi.1005697> and Prem et al. <doi:10.1371/journal.pcbi.1009098>. Provides easy access to contact data for 177 countries, for use in epidemiological, demographic or social sciences research.

Last updated

demographicsepidemiologysocial-sciences

5.56 score 11 stars 22 scripts 474 downloads

remart - Reimplementation of the 'biomaRt' Package Using Modern Ensembl APIs

This package aims to offer a drop-in replacement to biomaRt using the same interface but the more modern and better maintained APIs provided by Ensembl. It provides an easy solution for compatibility with minimal changes for existing projects and packages. New projects may prefer to use another approach which is not constrained by the need for backward compatibility with biomaRt.

Last updated

annotationdataimport

4.98 score 7 stars 4 scripts

remart - Reimplementation of the 'biomaRt' Package Using Modern Ensembl APIs

This package aims to offer a drop-in replacement to biomaRt using the same interface but the more modern and better maintained APIs provided by Ensembl. It provides an easy solution for compatibility with minimal changes for existing projects and packages. New projects may prefer to use another approach which is not constrained by the need for backward compatibility with biomaRt.

Last updated

annotationdataimport

4.98 score 7 stars 4 scripts

mcmcensemble - Ensemble Sampler for Affine-Invariant MCMC

Provides ensemble samplers for affine-invariant Monte Carlo Markov Chain, which allow a faster convergence for badly scaled estimation problems. Two samplers are proposed: the 'differential.evolution' sampler from ter Braak and Vrugt (2008) <doi:10.1007/s11222-008-9104-9> and the 'stretch' sampler from Goodman and Weare (2010) <doi:10.2140/camcos.2010.5.65>.

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mcmcmcmc-sampler

4.92 score 2 stars 21 scripts 333 downloads

romeo - Minimal R 'OME-Zarr' Reader

A minimal R package to reading, writing and validating multiscale OME-Zarr images.

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dataimport

4.62 score 7 stars 4 scripts

romeo - Minimal R 'OME-Zarr' Reader

A minimal R package to reading, writing and validating multiscale OME-Zarr images.

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dataimport

4.62 score 7 stars 4 scripts

authoritative - Parse and Deduplicate Author Names

Utilities to parse authors fields from DESCRIPTION files and general purpose functions to deduplicate names in database, beyond the specific case of R package authors.

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data-cleaningdata-extraction

4.30 score 9 scripts 325 downloads

numberize - Convert Words to Numbers in Multiple Languages

Converts written out numbers into their equivalent numbers. Supports numbers written out in English, French, or Spanish.

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r-programming

4.26 score 4 stars 1 dependents 3 scripts 363 downloads

remart - Reimplementation of the 'biomaRt' Package Using Modern Ensembl APIs

This package aims to offer a drop-in replacement to biomaRt using the same interface but the more modern and better maintained APIs provided by Ensembl. It provides an easy solution for compatibility with minimal changes for existing projects and packages. New projects may prefer to use another approach which is not constrained by the need for backward compatibility with biomaRt.

Last updated

annotationdataimport

4.13 score 4 scripts