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r-pcit
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public |
Apply Partial Correlation coefficient with Information Theory (PCIT) to a correlation matrix. The PCIT algorithm identifies meaningful correlations to define edges in a weighted network. The algorithm can be applied to any correlation-based network including but not limited to gene co-expression networks. To reduce compute time by making use of multiple compute cores, simply run PCIT on a computer with has multiple cores and also has the Rmpi package installed. PCIT will then auto-detect the multicore environment and run in parallel mode without the need to rewrite your scripts. This makes scripts, using PCIT, portable across single core (or no Rmpi package installed) computers which will run in serial mode and multicore (with Rmpi package installed) computers which will run in parallel mode.
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2025-04-22 |
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r-icluster
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public |
Integrative clustering of multiple genomic data types using a joint latent variable model.
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2025-04-22 |
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r-filehash
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public |
Implements a simple key-value style database where character string keys are associated with data values that are stored on the disk. A simple interface is provided for inserting, retrieving, and deleting data from the database. Utilities are provided that allow 'filehash' databases to be treated much like environments and lists are already used in R. These utilities are provided to encourage interactive and exploratory analysis on large datasets. Three different file formats for representing the database are currently available and new formats can easily be incorporated by third parties for use in the 'filehash' framework.
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2025-04-22 |
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r-argumentcheck
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The typical process of checking arguments in functions is iterative. In this process, an error may be returned and the user may fix it only to receive another error on a different argument. 'ArgumentCheck' facilitates a more helpful way to perform argument checks allowing the programmer to run all of the checks and then return all of the errors and warnings in a single message.
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2025-04-22 |
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powerline-status
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public |
Powerline is a statusline plugin for vim
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2025-04-22 |
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r-squash
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public |
Functions for color-based visualization of multivariate data, i.e. colorgrams or heatmaps. Lower-level functions map numeric values to colors, display a matrix as an array of colors, and draw color keys. Higher-level plotting functions generate a bivariate histogram, a dendrogram aligned with a color-coded matrix, a triangular distance matrix, and more.
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2025-04-22 |
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r-sme
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public |
Fit smoothing-splines mixed-effects models to replicated functional data sets and visualise the results.
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2025-04-22 |
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r-scrm
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public |
A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution. Different to other coalescent based simulations, it has an optional approximation parameter that allows for high accuracy while maintaining a linear run time cost for long sequences. It is optimized for simulating massive data sets as produced by Next- Generation Sequencing technologies for up to several thousand sequences.
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2025-04-22 |
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r-ruv
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public |
Implements the 'RUV' (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. These algorithms were proposed in Gagnon-Bartsch and Speed (2012) <doi:10.1093/nar/gkz433>, Gagnon-Bartsch, Jacob and Speed (2013), and Molania, et. al. (2019) <doi:10.1093/nar/gkz433>. The algorithms require the user to specify a set of negative control variables, as described in the references. The algorithms included in this package are 'RUV-2', 'RUV-4', 'RUV-inv', 'RUV-rinv', 'RUV-I', and RUV-III', along with various supporting algorithms.
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2025-04-22 |
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r-rematch2
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public |
Wrappers on 'regexpr' and 'gregexpr' to return the match results in tidy data frames.
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2025-04-22 |
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r-princurve
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public |
Fitting a principal curve to a data matrix in arbitrary dimensions. Hastie and Stuetzle (1989) <doi:10.2307/2289936>.
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2025-04-22 |
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r-pdist
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public |
Computes the euclidean distance between rows of a matrix X and rows of another matrix Y. Previously, this could be done by binding the two matrices together and calling 'dist', but this creates unnecessary computation by computing the distances between a row of X and another row of X, and likewise for Y. pdist strictly computes distances across the two matrices, not within the same matrix, making computations significantly faster for certain use cases.
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2025-04-22 |
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r-nls2
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public |
Adds brute force and multiple starting values to nls.
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2025-04-22 |
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r-apcluster
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public |
Implements Affinity Propagation clustering introduced by Frey and Dueck (2007) <DOI:10.1126/science.1136800>. The algorithms are largely analogous to the 'Matlab' code published by Frey and Dueck. The package further provides leveraged affinity propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.
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2025-04-22 |
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r-fingerprint
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public |
Functions to manipulate binary fingerprints of arbitrary length. A fingerprint is represented by an object of S4 class 'fingerprint' which is internally represented a vector of integers, such that each element represents the position in the fingerprint that is set to 1. The bitwise logical functions in R are overridden so that they can be used directly with 'fingerprint' objects. A number of distance metrics are also available (many contributed by Michael Fadock). Fingerprints can be converted to Euclidean vectors (i.e., points on the unit hypersphere) and can also be folded using OR. Arbitrary fingerprint formats can be handled via line handlers. Currently handlers are provided for CDK, MOE and BCI fingerprint data.
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2025-04-22 |
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r-alluvial
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public |
Creating alluvial diagrams (also known as parallel sets plots) for multivariate and time series-like data.
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2025-04-22 |
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r-colortools
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public |
R package with handy functions to help users select and play with color schemes in an HSV color model
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2025-04-22 |
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r-heatmap3
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public |
An improved heatmap package. Completely compatible with the original R function 'heatmap', and provides more powerful and convenient features.
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2025-04-22 |
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r-plasmidprofiler
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public |
Contains functions developed to combine the results of querying a plasmid database using short-read sequence typing with the results of a blast analysis against the query results.
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2025-04-22 |
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r-parmigene
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public |
Parallel estimation of the mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for the reconstruction of gene regulatory networks (Sales et al, 2011 <doi:10.1093/bioinformatics/btr274>).
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2025-04-22 |
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r-shinyfiles
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public |
Provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to "download" files to a temporary location. Both file and folder selection as well as file saving is available.
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2025-04-22 |
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r-robustrankaggreg
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public |
Methods for aggregating ranked lists, especially lists of genes. It implements the Robust Rank Aggregation (Kolde et. al in preparation) and some other simple algorithms for the task. RRA method uses a probabilistic model for aggregation that is robust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking.
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2025-04-22 |
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r-reportr
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Provides a system for reporting messages, which provides certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, assertions, expression substitution, automatic generation of stack traces for debugging, and conditional reporting based on the current "output level".
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2025-04-22 |
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r-pinfsc50
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public |
Genomic data for the plant pathogen "Phytophthora infestans." It includes a variant file ('VCF'), a sequence file ('FASTA') and an annotation file ('GFF'). This package is intended to be used as example data for packages that work with genomic data.
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2025-04-22 |
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r-nnls
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An R interface to the Lawson-Hanson implementation of an algorithm for non-negative least squares (NNLS). Also allows the combination of non-negative and non-positive constraints.
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2025-04-22 |
