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ez_setup
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public |
ez_setup.py and distribute_setup.py
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2025-04-22 |
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filesdb
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public |
A simple tool for tracking files
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2025-04-22 |
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django-unique-upload
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public |
A django utility that creates unique file names for uploaded files via uuids.
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2025-04-22 |
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django-configurations
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public |
A helper for organizing Django settings.
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2025-04-22 |
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r-flowr
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public |
This framework allows you to design and implement complex pipelines, and deploy them on your institution's computing cluster. This has been built keeping in mind the needs of bioinformatics workflows. However, it is easily extendable to any field where a series of steps (shell commands) are to be executed in a (work)flow.
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2025-04-22 |
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r-diagram
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public |
Visualises simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualising webs, electrical networks, etc. Support for the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter M.J. Herman (2009), Springer. and the book "Solving Differential Equations in R" by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012), Springer. Includes demo(flowchart), demo(plotmat), demo(plotweb).
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2025-04-22 |
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r-circlize
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public |
Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data.
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2025-04-22 |
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r-getoptlong
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public |
This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.
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2025-04-22 |
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r-fpc
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public |
Various methods for clustering and cluster validation. Fixed point clustering. Linear regression clustering. Clustering by merging Gaussian mixture components. Symmetric and asymmetric discriminant projections for visualisation of the separation of groupings. Cluster validation statistics for distance based clustering including corrected Rand index. Standardisation of cluster validation statistics by random clusterings and comparison between many clustering methods and numbers of clusters based on this. Cluster-wise cluster stability assessment. Methods for estimation of the number of clusters: Calinski-Harabasz, Tibshirani and Walther's prediction strength, Fang and Wang's bootstrap stability. Gaussian/multinomial mixture fitting for mixed continuous/categorical variables. Variable-wise statistics for cluster interpretation. DBSCAN clustering. Interface functions for many clustering methods implemented in R, including estimating the number of clusters with kmeans, pam and clara. Modality diagnosis for Gaussian mixtures. For an overview see package?fpc.
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2025-04-22 |
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r-shape
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public |
Functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows,
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2025-04-22 |
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r-prabclus
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public |
Distance-based parametric bootstrap tests for clustering with spatial neighborhood information. Some distance measures, Clustering of presence-absence, abundance and multilocus genetical data for species delimitation, nearest neighbor based noise detection. Genetic distances between communities. Tests whether various distance-based regressions are equal. Try package?prabclus for on overview.
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2025-04-22 |
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r-params
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public |
An interface to simplify organizing parameters used in a package, using external configuration files. This attempts to provide a cleaner alternative to options().
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2025-04-22 |
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r-mclust
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public |
Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference.
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2025-04-22 |
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r-kernlab
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public |
Kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods 'kernlab' includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.
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2025-04-22 |
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r-globaloptions
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public |
It provides more controls on the option values such as validation and filtering on the values, making options invisible or private.
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2025-04-22 |
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r-flexmix
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public |
A general framework for finite mixtures of regression models using the EM algorithm is implemented. The E-step and all data handling are provided, while the M-step can be supplied by the user to easily define new models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering.
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2025-04-22 |
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r-relations
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public |
Data structures and algorithms for k-ary relations with arbitrary domains, featuring relational algebra, predicate functions, and fitters for consensus relations.
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2025-04-22 |
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w3m
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public |
Text mode web browser/pager.
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2025-04-22 |
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segno
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public |
Segno is a QR Code and Micro QR Code encoder which has no further dependencies.
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2025-04-22 |
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r-sets
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public |
Data structures and basic operations for ordinary sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets, customizable sets, and intervals.
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2025-04-22 |
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r-preseqr
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public |
Originally as an R version of Preseq <doi:10.1038/nmeth.2375>, the package has extended its functionality to predict the r-species accumulation curve (r-SAC), which is the number of species represented at least r times as a function of the sampling effort. When r = 1, the curve is known as the species accumulation curve, or the library complexity curve in high-throughput genomic sequencing. The package includes both parametric and nonparametric methods, as described by Deng C, et al. (2018) <arXiv:1607.02804v3>.
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2025-04-22 |
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r-rniftyreg
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public |
Provides an 'R' interface to the 'NiftyReg' image registration tools <http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration are supported, in two and three dimensions.
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2025-04-22 |
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r-polynom
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public |
A collection of functions to implement a class for univariate polynomial manipulations.
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2025-04-22 |
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r-ore
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public |
Provides an alternative to R's built-in functionality for handling regular expressions, based on the Onigmo library. Offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.
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2025-04-22 |
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r-segmented
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public |
Given a regression model, segmented `updates' it by adding one or more segmented (i.e., piece-wise linear) relationships. Several variables with multiple breakpoints are allowed. The estimation method is discussed in Muggeo (2003, <doi:10.1002/sim.1545>) and illustrated in Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>). An approach for hypothesis testing is presented in Muggeo (2016, <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>).
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2025-04-22 |
