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r-bayesant
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public |
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.
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2025-04-03 |
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r-funguildr
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public |
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.
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2025-04-01 |
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fastqindex
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public |
No Summary
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2025-03-25 |
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unittest-cpp
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public |
No Summary
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2025-03-25 |
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r-qs2
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public |
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.
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2025-03-25 |
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r-optimotu.pipeline
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public |
Pipeline for environmental DNA metabarcoding
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2025-03-25 |
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r-igraph
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public |
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.
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2025-03-25 |
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r-secretbase
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public |
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/>.
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2025-03-25 |
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r-crew.cluster
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public |
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>.
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2025-03-25 |
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nng
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public |
nanomsg-next-generation -- light-weight brokerless messaging
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2025-03-25 |
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r-ecmwfr
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public |
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.
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2025-03-25 |
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r-crew
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public |
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>.
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2025-03-25 |
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r-getip
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public |
A micro-package for getting your 'IP' address, either the local/internal or the public/external one. Currently only 'IPv4' addresses are supported.
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2025-03-25 |
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r-mirai
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public |
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).
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2025-03-25 |
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r-nanonext
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public |
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.
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2025-03-25 |
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r-optimotu
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public |
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.
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2025-03-25 |
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pifcosm
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public |
PisCoSm is a pipline to construct supermatrix trees from GenBank data
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2025-03-25 |
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r-trackdown
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public |
Collaborative writing and editing of R Markdown (or Sweave) documents. The local .Rmd (or .Rnw) is uploaded as a plain-text file to Google Drive. By taking advantage of the easily readable Markdown (or LaTeX) syntax and the well-known online interface offered by Google Docs, collaborators can easily contribute to the writing and editing process. After integrating all authors’ contributions, the final document can be downloaded and rendered locally.
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2025-03-25 |
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r-hues
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public |
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.
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2025-03-25 |
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gefast
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public |
Clustering tool using Swarm's clustering strategy and Pass-Join's segment filter.
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2025-03-25 |
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r-tarchetypes
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public |
Function-oriented Make-like declarative workflows for Statistics and data science are supported in the 'targets' R package. As an extension to 'targets', the 'tarchetypes' package provides convenient user-side functions to make 'targets' easier to use. By establishing reusable archetypes for common kinds of targets and pipelines, these functions help express complicated reproducible workflows concisely and compactly. The methods in this package were influenced by the 'drake' R package by Will Landau (2018) <doi:10.21105/joss.00550>.
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2025-03-25 |
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r-targets
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public |
As a pipeline toolkit for Statistics and data science in R, the 'targets' package brings together function-oriented programming and 'Make'-like declarative workflows. It analyzes the dependency relationships among the tasks of a workflow, skips steps that are already up to date, runs the necessary computation with optional parallel workers, abstracts files as R objects, and provides tangible evidence that the results match the underlying code and data. The methodology in this package borrows from GNU 'Make' (2015, ISBN:978-9881443519) and 'drake' (2018, <doi:10.21105/joss.00550>).
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2025-03-25 |
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r-phylotax
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public |
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.
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2025-03-25 |
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r-metacoder
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public |
A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy).
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2025-03-25 |
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r-deming
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public |
Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions.
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2025-03-25 |
