| r-optimotu.pipeline | 0.6.1 | More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description. | Feb 13, 2026 | MIT |
| fastqindex | 0.9.0b | — | Mar 25, 2025 | — |
| 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 |
| unittest-cpp | 2.0.0 | — | Mar 25, 2025 | — |
| r-qs2 | 0.1.4 | Streamlines and accelerates the process of saving and loading R objects, improving speed and compression compared to other methods. The package provides two compression formats: the 'qs2' format, which uses R serialization via the C API while optimizing compression and disk I/O, and the 'qdata' format, featuring custom serialization for slightly faster performance and better compression. Additionally, the 'qs2' format can be directly converted to the standard 'RDS' format, ensuring long-term compatibility with future versions of R. | Mar 25, 2025 | GPL-3.0-only |
| 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-secretbase | 0.2.0 | SHA-3 cryptographic hash and SHAKE256 extendable-output functions (XOF). The SHA-3 Secure Hash Standard was published by the National Institute of Standards and Technology (NIST) in 2015 at <doi:10.6028/NIST.FIPS.202>. Fast and memory-efficient implementation using the core algorithm from 'Mbed TLS' under the Trusted Firmware Project <https://www.trustedfirmware.org/projects/mbed-tls/>. | Mar 25, 2025 | GPL-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-optimotu | 0.9.4 | OptimOTU calculates single-linkage clusters at multiple thresholds given a distance matrix, which may be sparse, using a fast, multithreaded C++ implementation. In particular, the memory requirements are small and fixed, and it can accept the distance matrix from a file or text connection, meaning that it can operate on very large matrices which do not fit in RAM. Routines for quickly counting the measure of the intersection of sorted sets, and for calculating the multiclass F-measure, are also included. | Feb 17, 2026 | MIT |
| 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-tzara | 0.0.11 | To reduce computational complexity, dada2 only uses non-singletons as seeds for denoising. For this strategy to work, each true sequence must be represented by at least two identical reads. Especially with long amplicons, the probability of two reads having exactly the same errors is much lower than the probability of being error-free, so in practice this means that each true sequence must have two error-free reads. This becomes problematic for rare sequences in long amplicon libraries. An alternative is to use hidden Markov models to cut out the most variable section of the targeted region and use dada2 to create denoised sequences using only that sequence, and then find a consensus sequence for all sequences that match the index region. Tzara (named after Tristan Tzara, a central figure in the Dada art movement) applies this method to rDNA sequences by cutting out the variable ITS2 region using rITSx. | Mar 25, 2025 | GPL-3 |
| 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 |
| bptp | 0.5.1 | bPTP: a Bayesian implementation of the PTP model for species delimitation. | Mar 25, 2025 | GPL3 |
| r-tikzdevice | 0.12 | Provides a graphics output device for R that records plots in a LaTeX-friendly format. The device transforms plotting commands issued by R functions into LaTeX code blocks. When included in a LaTeX document, these blocks are interpreted with the help of 'TikZ'---a graphics package for TeX and friends written by Till Tantau. Using the 'tikzDevice', the text of R plots can contain LaTeX commands such as mathematical formula. The device also allows arbitrary LaTeX code to be inserted into the output stream. | Mar 25, 2025 | GPL (>= 2) |
| r-ritsx | 0.0.5 | This package is an interface to the ITSx command-line utility (http://microbiology.se/software/itsx/) from R. | Mar 25, 2025 | GPL-3 |
| 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-nanonext | 1.1.0 | R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is a socket library implementing 'Scalability Protocols', a reliable, high-performance standard for common communications patterns including publish/subscribe, request/reply and service discovery, over in-process, IPC, TCP, WebSocket and secure TLS transports. As its own threaded concurrency framework, provides a toolkit for asynchronous programming and distributed computing, with intuitive 'aio' objects which resolve automatically upon completion of asynchronous operations, and synchronisation primitives allowing R to wait upon events signalled by concurrent threads. | Mar 25, 2025 | GPL-3.0-or-later |
| r-monetdblite | 0.6.0 | In-Process Version of 'MonetDB'. | Mar 25, 2025 | MPL |
| r-phylotax | 0.0.4 | Combines taxonomic assignments made with different methods or databases using a phylogenetic tree. Clades within the tree are assigned to a taxon if the assignment is consistent with at least one result for all of the members of the clade, except the members that do not have any assignments at all. This resolves conflict between different methods, while also adding assignments to unknown sequences which are nested in an identified clade. The package also includes helper functions to assign taxonomy using several methods, and compile the results into a uniform format. | Mar 25, 2025 | GPL-3 |
| 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-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-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-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-mirai | 0.12.1 | Lightweight parallel code execution and distributed computing. Designed for simplicity, a 'mirai' evaluates an R expression asynchronously, on local or network resources, resolving automatically upon completion. Efficient scheduling over fast inter-process communications or secure TLS connections over TCP/IP, built on 'nanonext' and 'NNG' (Nanomsg Next Gen). | Mar 25, 2025 | GPL-3.0-or-later |
| r-restez | 1.0.0 | Download large sections of 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and generate a local SQL-based database. A user can then query this database using 'restez' functions or through 'rentrez' <https://CRAN.R-project.org/package=rentrez> wrappers. | Mar 25, 2025 | MIT + file LICENSE |
