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psborrow2 - Bayesian Dynamic Borrowing Analysis and Simulation

Bayesian dynamic borrowing is an approach to incorporating external data to supplement a randomized, controlled trial analysis in which external data are incorporated in a dynamic way (e.g., based on similarity of outcomes); see Viele 2013 <doi:10.1002/pst.1589> for an overview. This package implements the hierarchical commensurate prior approach to dynamic borrowing as described in Hobbes 2011 <doi:10.1111/j.1541-0420.2011.01564.x>. There are three main functionalities. First, 'psborrow2' provides a user-friendly interface for applying dynamic borrowing on the study results handles the Markov Chain Monte Carlo sampling on behalf of the user. Second, 'psborrow2' provides a simulation framework to compare different borrowing parameters (e.g. full borrowing, no borrowing, dynamic borrowing) and other trial and borrowing characteristics (e.g. sample size, covariates) in a unified way. Third, 'psborrow2' provides a set of functions to generate data for simulation studies, and also allows the user to specify their own data generation process. This package is designed to use the sampling functions from 'cmdstanr' which can be installed from <https://stan-dev.r-universe.dev>.

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bayesian-dynamic-borrowingpsborrow2simulation-study

7.41 score 22 stars 29 scripts 376 downloads

BiocDuckDB - Bioconductor DuckDB Integration and High-Level I/O

Integration package providing high-level Parquet I/O functions and optimized methods for single-cell analysis workflows using DuckDB-backed data structures. Includes readParquet and writeParquet functions for seamless serialization of SummarizedExperiment, SingleCellExperiment, MultiAssayExperiment, and MultiAssaySpatialExperiment objects, plus SQL-optimized implementations of scran and scuttle methods for variance modeling, marker detection, QC metrics, and normalization. This package brings together DuckDBDataFrame, DuckDBArray, DuckDBGRanges, and DuckDBSpatial (optional) for complete Bioconductor integration.

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dataimportdatarepresentationinfrastructurernaseqsequencingsinglecellsoftware

6.70 score 5 stars 37 scripts 131 downloads

DuckDBDataFrame - DuckDB-Backed DataFrame and Table Structures

Provides DuckDB-backed implementations of core tabular data structures including DuckDBTable, DuckDBDataFrame, and DuckDBColumn. These classes extend Bioconductor's S4Vectors framework to enable efficient, out-of-memory operations on large tabular datasets using DuckDB's analytical database engine. The package includes SQL function discovery, connection management, and support for list columns and embeddings stored in ARRAY[] columns.

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dataimportdatarepresentationinfrastructuresoftware

6.57 score 1 stars 4 dependents 14 scripts 206 downloads

DuckDBArray - DuckDB-Backed DelayedArray Implementation

Provides DuckDB-backed implementations of DelayedArray and DelayedMatrix classes for efficient, out-of-memory operations on large array and matrix datasets. The package includes DuckDBArray, DuckDBArraySeed, and DuckDBMatrix classes with optimized matrixStats methods. Supports sparse arrays, grid partitioning, and parallel processing for scalable genomic data analysis.

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dataimportdatarepresentationinfrastructuresoftware

6.31 score 1 dependents 18 scripts 306 downloads

MultiAssaySpatialExperiment - Multi-Assay Experiment with Spatial Context

Extends MultiAssayExperiment with spatial context elements (images, labels, points, shapes) for integrative analysis of spatially resolved multi-omics data. Supports coercion to and from SpatialExperiment and SpatialFeatureExperiment.

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infrastructuredatarepresentationspatial

6.02 score 1 dependents 9 scripts 117 downloads

DuckDBGRanges - DuckDB-Backed GenomicRanges Implementation

Provides DuckDB-backed implementations of GenomicRanges data structures for efficient, out-of-memory operations on large genomic interval datasets. The package includes DuckDBGRanges and DuckDBGRangesList classes with optimized range operations including restrict, flank, shift, findOverlaps, coverage, and distance calculations. Ideal for variant analysis, scATAC-seq peak analysis, and other genomic workflows requiring memory-efficient range operations on large datasets.

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dataimportdatarepresentationinfrastructuresequencingsoftware

5.83 score 1 dependents 8 scripts 200 downloads

DuckDBSpatial - DuckDB-Backed Spatial Data Structures

Provides DuckDB-backed implementations of spatial data structures for efficient out-of-memory operations on large spatial datasets. The package includes 68 sf-compatible spatial methods (st_intersects, st_contains, st_within, etc.) and GeoParquet 1.0 I/O support via writeGeoParquet(). Ideal for spatial analysis, genomic interval analysis, and integration with BiocDuckDB for MultiAssaySpatialExperiment workflows requiring memory-efficient operations on large datasets.

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dataimportdatarepresentationinfrastructuresoftware

5.48 score 2 stars 9 scripts 132 downloads

BayesERtools - Bayesian Exposure-Response Analysis Tools

Suite of tools that facilitate exposure-response analysis using Bayesian methods. The package provides a streamlined workflow for fitting types of models that are commonly used in exposure-response analysis - linear and Emax for continuous endpoints, logistic linear and logistic Emax for binary endpoints, as well as performing simulation and visualization. Learn more about the workflow at <https://genentech.github.io/BayesERbook/>.

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5.30 score 8 stars 536 downloads