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r-orcme
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public |
Provides clustering of genes with similar dose response (or time course) profiles. It implements the method described by Lin et al. (2012).
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2025-04-22 |
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r-oriclust
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public |
ORIClust is a user-friendly R-based software package for gene clustering. Clusters are given by genes matched to prespecified profiles across various ordered treatment groups. It is particularly useful for analyzing data obtained from short time-course or dose-response microarray experiments.
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2025-04-22 |
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r-goric
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public |
Generalized Order-Restricted Information Criterion (GORIC) value for a set of hypotheses in multivariate linear models and generalised linear models.
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2025-04-22 |
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r-fd
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public |
FD is a package to compute different multidimensional FD indices. It implements a distance-based framework to measure FD that allows any number and type of functional traits, and can also consider species relative abundances. It also contains other useful tools for functional ecology.
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2025-04-22 |
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r-openimager
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public |
Incorporates functions for image preprocessing, filtering and image recognition. The package takes advantage of 'RcppArmadillo' to speed up computationally intensive functions. The histogram of oriented gradients descriptor is a modification of the 'findHOGFeatures' function of the 'SimpleCV' computer vision platform, the average_hash(), dhash() and phash() functions are based on the 'ImageHash' python library. The Gabor Feature Extraction functions are based on 'Matlab' code of the paper, "CloudID: Trustworthy cloud-based and cross-enterprise biometric identification" by M. Haghighat, S. Zonouz, M. Abdel-Mottaleb, Expert Systems with Applications, vol. 42, no. 21, pp. 7905-7916, 2015, <doi:10.1016/j.eswa.2015.06.025>. The 'SLIC' and 'SLICO' superpixel algorithms were explained in detail in (i) "SLIC Superpixels Compared to State-of-the-art Superpixel Methods", Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 34, num. 11, p. 2274-2282, May 2012, <doi:10.1109/TPAMI.2012.120> and (ii) "SLIC Superpixels", Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, EPFL Technical Report no. 149300, June 2010.
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2025-04-22 |
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twofish
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public |
Bindings for the Twofish implementation by Niels Ferguson
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2025-04-22 |
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xeus-cling
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public |
Cling-based C++ kernel for Jupyter based on xeus
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2025-04-22 |
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opentsne
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public |
Extensible, parallel implementations of t-SNE
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2025-04-22 |
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xeus-python
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public |
A Jupyter kernel for the Python programming language based on Xeus
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2025-04-22 |
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r-soniclength
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public |
Estimate the abundance of cell clones from the distribution of lengths of DNA fragments (as created by sonication, whence `sonicLength'). The algorithm in "Estimating abundances of retroviral insertion sites from DNA fragment length data" by Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD. Bioinformatics; 2012 Mar 15;28(6):755-62 is implemented. The experimental setting and estimation details are described in detail there. Briefly, integration of new DNA in a host genome (due to retroviral infection or gene therapy) can be tracked using DNA sequencing, potentially allowing characterization of the abundance of individual cell clones bearing distinct integration sites. The locations of integration sites can be determined by fragmenting the host DNA (via sonication or fragmentase), breaking the newly integrated DNA at a known sequence, amplifying the fragments containing both host and integrated DNA, sequencing those amplicons, then mapping the host sequences to positions on the reference genome. The relative number of fragments containing a given position in the host genome estimates the relative abundance of cells hosting the corresponding integration site, but that number is not available and the count of amplicons per fragment varies widely. However, the expected number of distinct fragment lengths is a function of the abundance of cells hosting an integration site at a given position and a certain nuisance parameter. The algorithm implicitly estimates that function to estimate the relative abundance.
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2025-04-22 |
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r-pathological
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public |
Utilities for paths, files and directories.
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2025-04-22 |
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r-coxboost
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public |
This package provides routines for fitting Cox models by likelihood based boosting for a single endpoint or in presence of competing risks
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2025-04-22 |
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r-bglr
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public |
Bayesian Generalized Linear Regression.
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2025-04-22 |
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r-eulerr
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public |
Generate area-proportional Euler diagrams using numerical optimization. An Euler diagram is a generalization of a Venn diagram, relaxing the criterion that all interactions need to be represented. Diagrams may be fit with ellipses and circles via a wide range of inputs and can be visualized in numerous ways.
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2025-04-22 |
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r-sys
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public |
Drop-in replacements for the base system2() function with fine control and consistent behavior across platforms. Supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. Arguments on Windows automatically get encoded and quoted to work on different locales.
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2025-04-22 |
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r-webutils
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public |
Parses http request data in application/json, multipart/form-data, or application/x-www-form-urlencoded format. Includes example of hosting and parsing html form data in R using either 'httpuv' or 'Rhttpd'.
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2025-04-22 |
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r-polylabelr
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A wrapper around the C++ library 'polylabel' from 'Mapbox', providing an efficient routine for finding the approximate pole of inaccessibility of a polygon, which usually serves as an excellent candidate for labeling of a polygon.
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2025-04-22 |
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r-tmvtnorm
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public |
Random number generation for the truncated multivariate normal and Student t distribution. Computes probabilities, quantiles and densities, including one-dimensional and bivariate marginal densities. Computes first and second moments (i.e. mean and covariance matrix) for the double-truncated multinormal case.
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2025-04-22 |
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r-xtensor
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R bindings for xtensor, the C++ tensor algebra library
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2025-04-22 |
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r-ggdistribute
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The 'ggdistribute' package is an extension for plotting posterior or other types of unimodal distributions that require overlaying information about a distribution's intervals. It makes use of the 'ggproto' system to extend 'ggplot2', providing additional "geoms", "stats", and "positions." The extensions integrate with existing 'ggplot2' layer elements.
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2025-04-22 |
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r-markovchain
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Functions and S4 methods to create and manage discrete time Markov chains more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of their structural proprieties) analysis are provided.
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2025-04-22 |
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monetdblite
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public |
MonetDBLite is a serverless SQL database that runs inside of your Python process and does not require the installation of any external software.
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2025-04-22 |
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r-boolnet
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public |
Provides methods to reconstruct and generate synchronous, asynchronous, probabilistic and temporal Boolean networks, and to analyze and visualize attractors in Boolean networks.
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2025-04-22 |
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r-xmisc
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public |
This is Xiaobei's miscellaneous classes and functions useful when developing R packages, particularly for OOP using R Reference Class.
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2025-04-22 |
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r-nnlasso
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public |
Estimates of coefficients of lasso penalized linear regression and generalized linear models subject to non-negativity constraints on the parameters using multiplicative iterative algorithm. Entire regularization path for a sequence of lambda values can be obtained. Functions are available for creating plots of regularization path, cross validation and estimating coefficients at a given lambda value. There is also provision for obtaining standard error of coefficient estimates.
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2025-04-22 |
