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schema-salad
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public |
Schema Annotations for Linked Avro Data (SALAD)
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2025-09-24 |
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r-flare
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public |
Provide the implementation of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear model. We adopt the alternating direction method of multipliers and convert the original optimization problem into a sequential L1 penalized least square minimization problem, which can be efficiently solved by linearization algorithm. A multi-stage screening approach is adopted for further acceleration. Besides the sparse linear model estimation, we also provide the extension of these Lasso variants to sparse Gaussian graphical model estimation including TIGER and CLIME using either L1 or adaptive penalty. Missing values can be tolerated for Dantzig selector and CLIME. The computation is memory-optimized using the sparse matrix output.
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2025-09-24 |
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pyoptsparse
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public |
Package for formulating and solving nonlinear constrained optimization problems.
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2025-09-24 |
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r-imager
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public |
Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.
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2025-09-24 |
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r-multbxxc
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public |
Contains auxiliary routines for influx software. This packages is not intended to be used directly. Influx was published here: Sokol et al. (2012) <doi:10.1093/bioinformatics/btr716>.
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2025-09-24 |
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r-gunifrac
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public |
A suite of methods for powerful and robust microbiome data analysis including data normalization, data simulation, community-level association testing and differential abundance analysis. It implements generalized UniFrac distances, Geometric Mean of Pairwise Ratios (GMPR) normalization, semiparametric data simulator, distance-based statistical methods, and feature-based statistical methods. The distance-based statistical methods include three extensions of PERMANOVA: (1) PERMANOVA using the Freedman-Lane permutation scheme, (2) PERMANOVA omnibus test using multiple matrices, and (3) analytical approach to approximating PERMANOVA p-value. Feature-based statistical methods include linear model-based permutation tests for differential abundance analysis of zero-inflated compositional data.
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2025-09-24 |
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r-superheat
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public |
A system for generating extendable and customizable heatmaps for exploring complex datasets, including big data and data with multiple data types.
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2025-09-24 |
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r-rmisc
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public |
The Rmisc library contains many functions useful for data analysis and utility operations.
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2025-09-24 |
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r-ezplot
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public |
Wrapper for the 'ggplot2' package that creates a variety of common charts (e.g. bar, line, area, ROC, waterfall, pie) while aiming to reduce typing.
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2025-09-24 |
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r-did
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public |
The standard Difference-in-Differences (DID) setup involves two periods and two groups -- a treated group and untreated group. Many applications of DID methods involve more than two periods and have individuals that are treated at different points in time. This package contains tools for computing average treatment effect parameters in Difference in Differences setups with more than two periods and with variation in treatment timing using the methods developed in Callaway and Sant'Anna (2021) <doi:10.1016/j.jeconom.2020.12.001>. The main parameters are group-time average treatment effects which are the average treatment effect for a particular group at a a particular time. These can be aggregated into a fewer number of treatment effect parameters, and the package deals with the cases where there is selective treatment timing, dynamic treatment effects, calendar time effects, or combinations of these. There are also functions for testing the Difference in Differences assumption, and plotting group-time average treatment effects.
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2025-09-24 |
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r-sigmajs
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public |
Interface to 'sigma.js' graph visualization library including animations, plugins and shiny proxies.
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2025-09-24 |
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r-plsrglm
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public |
Provides (weighted) Partial least squares Regression for generalized linear models and repeated k-fold cross-validation of such models using various criteria. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
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2025-09-24 |
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gsshapyorm
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public |
SQLAlchemy Object Relational Model for GSSHA model files.
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2025-09-24 |
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r-forestly
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public |
Interactive forest plot for clinical trial safety analysis using 'metalite', 'reactable', 'plotly', and Analysis Data Model (ADaM) datasets. Includes functionality for adverse event filtering, incidence-based group filtering, hover-over reveals, and search and sort operations. The workflow allows for metadata construction, data preparation, output formatting, and interactive plot generation.
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2025-09-24 |
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r-ggnetwork
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public |
Geometries to plot network objects with 'ggplot2'.
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2025-09-24 |
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r-tsoutliers
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public |
Detection of Outliers in Time Series.
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2025-09-24 |
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r-qqman
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public |
Create Q-Q and manhattan plots for GWAS data from PLINK results.
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2025-09-24 |
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r-configr
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public |
Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
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2025-09-24 |
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r-neo4r
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public |
A Modern and Flexible 'Neo4J' Driver, allowing you to query data on a 'Neo4J' server and handle the results in R. It's modern in the sense it provides a driver that can be easily integrated in a data analysis workflow, especially by providing an API working smoothly with other data analysis and graph packages. It's flexible in the way it returns the results, by trying to stay as close as possible to the way 'Neo4J' returns data. That way, you have the control over the way you will compute the results. At the same time, the result is not too complex, so that the "heavy lifting" of data wrangling is not left to the user.
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2025-09-24 |
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libarrow-all
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public |
C++ libraries for Apache Arrow
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2025-09-24 |
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arrow-utils
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public |
Executables for manipulating Apache arrow files
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2025-09-24 |
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libparquet
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public |
C++ libraries for Apache Parquet
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2025-09-24 |
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libarrow-substrait
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public |
C++ libraries for Apache Arrow Substrait
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2025-09-24 |
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parquet-utils
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public |
Executables for inspecting Apache Parquet files
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2025-09-24 |
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libarrow-acero
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public |
C++ libraries for Apache Arrow Acero
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2025-09-24 |
