| bptp | 0.5.1 | bPTP: a Bayesian implementation of the PTP model for species delimitation. | Mar 25, 2025 | GPL3 |
| fastqindex | 0.9.0b | — | Mar 25, 2025 | — |
| gefast | 2.0.1 | Clustering tool using Swarm's clustering strategy and Pass-Join's segment filter. | Mar 25, 2025 | AGPL |
| nng | 1.6.0 | nanomsg-next-generation -- light-weight brokerless messaging | Mar 25, 2025 | MIT |
| pifcosm | 0.1.1 | PisCoSm is a pipline to construct supermatrix trees from GenBank data | Mar 25, 2025 | GPL-3.0-only |
| r-bayesant | 1.0.1 | BayesANT is a package for the taxonomic classification of DNA sequences. It trains a taxonomic classifier on a dataset of DNA barcodes and returns probabilistic predictions for query DNA sequences. BayesANT explicitly accounts for potential taxonomic novelty of the query sequences by relying on Bayesian nonparametric species sampling priors to model the taxonomic tree. | Oct 15, 2025 | MIT |
| r-crew | 0.9.0 | In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'NNG'-powered 'mirai' R package by Gao (2023) <https://CRAN.R-project.org/package=mirai> is a sleek and sophisticated scheduler that efficiently processes these intense workloads. The 'crew' package extends 'mirai' with a unifying interface for third-party worker launchers. Inspiration also comes from packages. 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischel, and Surmann (2017) <doi:10.21105/joss.00135>. | Mar 25, 2025 | MIT |
| r-crew.cluster | 0.3.0 | In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'crew.cluster' package extends the 'mirai'-powered 'crew' package with worker launcher plugins for traditional high-performance computing systems. Inspiration also comes from packages 'mirai' by Gao (2023) <https://github.com/shikokuchuo/mirai>, 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischl, and Surmann (2017). <doi:10.21105/joss.00135>. | Mar 25, 2025 | MIT |
| r-dada2 | 1.12.1 | The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching. | Mar 25, 2025 | LGPL-3 |
| r-deming | 1.4 | Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions. | Mar 25, 2025 | LGPL-2.0-or-later |
| r-disk.frame | 0.3.6 | A disk-based data manipulation tool for working with large-than-RAM datasets. Aims to lower the barrier-to-entry for manipulating large datasets by adhering closely to popular and familiar data manipulation paradigms like dplyr verbs and data.table syntax. | Mar 25, 2025 | MIT |
| r-ecmwfr | 1.5.0 | Programmatic interface to the European Centre for Medium-Range Weather Forecasts dataset web services (ECMWF; <https://www.ecmwf.int/>) and Copernicus's Climate Data Store (CDS; <https://cds.climate.copernicus.eu>). Allows for easy downloads of weather forecasts and climate reanalysis data in R. | Mar 25, 2025 | AGPL-3 |
| r-fst | 0.9.2 | Multithreaded serialization of compressed data frames using the 'fst' format. The 'fst' format allows for random access of stored data and compression with the LZ4 and ZSTD compressors created by Yann Collet. The ZSTD compression library is owned by Facebook Inc. | Mar 25, 2025 | AGPL-3.0-only |
| r-funguildr | 0.3.0 | This is a simple reimplementation of FUNGuild_v1.1.py. It queries the FUNGuild or NEMAGuild databases (http://www.stbates.org/guilds/app.php) and assigns trait information based on matching to a taxonomic classification. It does not include a copy of the FUNGuild or NEMAGuild databases, because they are continually updated as new information is submitted, but it does have methods to download them and store them as R objects to speed up repeated queries or to allow local queries without internet access. | Oct 15, 2025 | GPL-3 |
| r-gender | 0.5.4 | Infers state-recorded gender categories from first names and dates of birth using historical datasets. By using these datasets instead of lists of male and female names, this package is able to more accurately infer the gender of a name, and it is able to report the probability that a name was male or female. GUIDELINES: This method must be used cautiously and responsibly. Please be sure to see the guidelines and warnings about usage in the 'README' or the package documentation. See Blevins and Mullen (2015) <http://www.digitalhumanities.org/dhq/vol/9/3/000223/000223.html>. | Mar 25, 2025 | MIT |
| r-getip | 0.1_3 | A micro-package for getting your 'IP' address, either the local/internal or the public/external one. Currently only 'IPv4' addresses are supported. | Mar 25, 2025 | BSD_2_clause |
| r-ggh4x | 0.1.2.1 | A 'ggplot2' extension that does a variety of little helpful things. The package extends 'ggplot2' facets through customisation, by setting individual scales per panel, resizing panels and providing nested facets. Also allows multiple colour and fill scales per plot. Also hosts a smaller collection of stats, geoms and axis guides. | Mar 25, 2025 | MIT |
| r-ggnomics | 0.1.1 | This package contains some extensions to ggplot2 and convenience functions. | Mar 25, 2025 | GPL-3 |
| r-greta | 0.3.1 | Write statistical models in R and fit them by MCMC and optimisation on CPUs and GPUs, using Google 'TensorFlow'. greta lets you write your own model like in BUGS, JAGS and Stan, except that you write models right in R, it scales well to massive datasets, and it’s easy to extend and build on. See the website for more information, including tutorials, examples, package documentation, and the greta forum. | Mar 25, 2025 | Apache License 2.0 |
| r-hues | 0.2.0 | Creating effective colour palettes for figures is challenging. This package generates and plot palettes of optimally distinct colours in perceptually uniform colour space, based on 'iwanthue' <http://tools.medialab.sciences-po.fr/iwanthue/>. This is done through k-means clustering of CIE Lab colour space, according to user-selected constraints on hue, chroma, and lightness. | Mar 25, 2025 | LGPL-3.0-or-later |
| r-igraph | 2.0.2 | Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more. | Mar 25, 2025 | GPL-2.0-or-later |
| r-inferrnal | 0.99.8 | Search for matches to a covariance model in RNA sequences, or align RNA sequences to a covariance model. Covariance models use a combination of primary structure (nucleotide sequence) and secondary structure (base pairing) to model non-protein-coding RNA families. This package is a thin wrapper around the Infernal package, which is not included and needs to be installed independently. Functions to read, write, and manipulate multiple sequence alignments in Stockholm format are also included. | Oct 15, 2025 | MIT |
| r-ipc | 0.1.3 | Provides tools for passing messages between R processes. Shiny Examples are provided showing how to perform useful tasks such as: updating reactive values from within a future, progress bars for long running async tasks, and interrupting async tasks based on user input. | Mar 25, 2025 | MIT + file LICENCE |
| r-lsux | 0.99.8 | LSUx is a tool to extract domains from rDNA using covariance models as implemented in the Infernal package. | Mar 25, 2025 | MIT |
| r-metacoder | 0.3.4 | A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy). | Mar 25, 2025 | GPL-2 | GPL-3 |
