|
r-rweblogo
|
public |
RWebLogo is a wrapper for the WebLogo python package that allows generating of customised sequence logos. Sequence logos are graphical representations of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences). Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.
|
2025-04-22 |
|
r-rwc
|
public |
Code to facilitate simulation and inference when connectivity is defined by underlying random walks. Methods for spatially-correlated pairwise distance data are especially considered. This provides core code to conduct analyses similar to that in Hanks and Hooten (2013) <doi:10.1080/01621459.2012.724647>.
|
2025-04-22 |
|
r-rwars
|
public |
Provides functions to retrieve and reformat data from the 'Star Wars' API (SWAPI) <https://swapi.co/>.
|
2025-04-22 |
|
r-rvtdt
|
public |
Used to compute population controls weighted rare variants transmission distortion test
|
2025-04-22 |
|
r-rviewgraph
|
public |
This is an 'R' interface to Alun Thomas's 'ViewGraph' 'Java' graph viewing program. It takes a graph specified as an incidence matrix, list of edges, or in 'igraph' format and runs a graphical user interface that shows an animation of a force directed algorithm positioning the vertices in two dimensions. It works well for graphs of various structure of up to a few thousand vertices. It's not fazed by graphs that comprise several components. The coordinates can be read as an 'igraph' style layout matrix at any time. The user can mess with the layout using a mouse, preferably one with 3 buttons, and some keyed commands. The 'Java' program 'ViewGraph' is contained in Alun Thomas's 'JPSGCS' collection of 'Java' programs for statistical genetics and computational statistics. The homepage for 'JPSGCS' is <http://www-genepi.med.utah.edu/~alun/software/index.html>. The documentation page for 'ViewGraph' is at <http://www-genepi.med.utah.edu/~alun/software/docs/ViewGraph.html>.
|
2025-04-22 |
|
r-rviennacl
|
public |
'ViennaCL' is a free open-source linear algebra library for computations on many-core architectures (GPUs, MIC) and multi-core CPUs. The library is written in C++ and supports 'CUDA', 'OpenCL', and 'OpenMP' (including switches at runtime). I have placed these libraries in this package as a more efficient distribution system for CRAN. The idea is that you can write a package that depends on the 'ViennaCL' library and yet you do not need to distribute a copy of this code with your package.
|
2025-04-22 |
|
r-rvhpdt
|
public |
To detecting rare variants for binary traits using general pedigrees, the pedigree disequilibrium tests are proposed by collapsing rare haplotypes/variants with/without weights. To run the test, MERLIN is needed in Linux for haplotyping.
|
2025-04-22 |
|
r-rvcheck
|
public |
Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').
|
2025-04-22 |
|
r-rv
|
public |
Implements a simulation-based random variable class and a suite of methods for extracting parts of random vectors, calculating extremes of random vectors, and generating random vectors under a variety of distributions following Kerman and Gelman (2007) <doi:10.1007/s11222-007-9020-4>.
|
2025-04-22 |
|
r-ruta
|
public |
Implementation of several unsupervised neural networks, from building their architecture to their training and evaluation. Available networks are auto-encoders including their main variants: sparse, contractive, denoising, robust and variational, as described in Charte et al. (2018) <doi:10.1016/j.inffus.2017.12.007>.
|
2025-04-22 |
|
r-runstats
|
public |
Provides methods for fast computation of running sample statistics for time series. These include: (1) mean, (2) standard deviation, and (3) variance over a fixed-length window of time-series, (4) correlation, (5) covariance, and (6) Euclidean distance (L2 norm) between short-time pattern and time-series. Implemented methods utilize Convolution Theorem to compute convolutions via Fast Fourier Transform (FFT).
|
2025-04-22 |
|
r-runiversal
|
public |
This package contains some functions for converting R objects to Java style variables and XML. Generated Java code is interpretable by dynamic Java libraries such as Beanshell. Calling R externally and handling the Java or XML output is an other way to call R from other languages without native interfaces. For a Java implementation of this approach visit http://www.mhsatman.com/rcaller.php and http://stdioe.blogspot.com/search/label/rcaller
|
2025-04-22 |
|
r-runit
|
public |
R functions implementing a standard Unit Testing framework, with additional code inspection and report generation tools.
|
2025-04-22 |
|
r-rtype
|
public |
A strong type system for R which supports symbol declaration and assignment with type checking and condition checking.
|
2025-04-22 |
|
r-rtwalk
|
public |
The 't-walk' is a general-purpose MCMC sampler for arbitrary continuous distributions that requires no tuning.
|
2025-04-22 |
|
r-rt.test
|
public |
Performs one-sample t-test based on robustified statistics using median/MAD (TA) and Hodges-Lehmann/Shamos (TB). For more details, see Park and Wang (2018)<arXiv:1807.02215>. This work was partially supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (No. NRF-2017R1A2B4004169).
|
2025-04-22 |
|
r-rtsplot
|
public |
A fast and elegant time series visualization package. In addition to the standard R plot types, this package supports candle sticks, open-high-low-close, and volume plots. Useful for visualizing any time series data, e.g., stock prices and technical indicators.
|
2025-04-22 |
|
r-rtson
|
public |
TSON, short for Typed JSON, is a binary-encoded serialization of JSON like document that support JavaScript typed data (https://github.com/tercen/TSON).
|
2025-04-22 |
|
r-rts
|
public |
This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
|
2025-04-22 |
|
r-rtrim
|
public |
The TRIM model is widely used for estimating growth and decline of animal populations based on (possibly sparsely available) count data. The current package is a reimplementation of the original TRIM software developed at Statistics Netherlands by Jeroen Pannekoek. See <https://www.cbs.nl/en-gb/society/nature-and-environment/indices-and-trends%2d%2dtrim%2d%2d> for more information about TRIM.
|
2025-04-22 |
|
r-rtorch
|
public |
'R' implementation and interface of the Machine Learning platform 'PyTorch' <https://pytorch.org/> developed in 'Python'. It requires a 'conda' environment with 'torch' and 'torchvision' to provide 'PyTorch' functions, methods and classes. The key object in 'PyTorch' is the tensor which is in essence a multidimensional array. These tensors are fairly flexible to perform calculations in CPUs as well as 'GPUs' to accelerate the process.
|
2025-04-22 |
|
r-rtnmin
|
public |
Truncated Newton function minimization with bounds constraints based on the 'Matlab'/'Octave' codes of Stephen Nash.
|
2025-04-22 |
|
r-rtika
|
public |
Extract text or metadata from over a thousand file types, using Apache Tika <https://tika.apache.org/>. Get either plain text or structured XHTML content.
|
2025-04-22 |
|
r-rticles
|
public |
A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.
|
2025-04-22 |
|
r-rtf
|
public |
A set of R functions to output Rich Text Format (RTF) files with high resolution tables and graphics that may be edited with a standard word processor such as Microsoft Word.
|
2025-04-22 |
