snpsettest - A Set-Based Association Test using GWAS Summary Statistics

The goal of 'snpsettest' is to provide simple tools that perform set-based association tests (e.g., gene-based association tests) using GWAS (genome-wide association study) summary statistics. A set-based association test in this package is based on the statistical model described in VEGAS (versatile gene-based association study), which combines the effects of a set of SNPs accounting for linkage disequilibrium between markers. This package uses a different approach from the original VEGAS implementation to compute set-level p values more efficiently, as described in <https://github.com/HimesGroup/snpsettest/wiki/Statistical-test-in-snpsettest>.

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openblascppopenmp

5.02 score 7 stars 9 scripts 264 downloads

qmtools - Quantitative Metabolomics Data Processing Tools

The qmtools (quantitative metabolomics tools) package provides basic tools for processing quantitative metabolomics data with the standard SummarizedExperiment class. This includes functions for imputation, normalization, feature filtering, feature clustering, dimension-reduction, and visualization to help users prepare data for statistical analysis. This package also offers a convenient way to compute empirical Bayes statistics for which metabolic features are different between two sets of study samples. Several functions in this package could also be used in other types of omics data.

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metabolomicspreprocessingnormalizationdimensionreductionmassspectrometry

4.72 score 2 stars 13 scripts 334 downloads

raqs - Interface to the US EPA Air Quality System (AQS) API

Offers functions for fetching JSON data from the US EPA Air Quality System (AQS) API with options to comply with the API rate limits. See <https://aqs.epa.gov/aqsweb/documents/data_api.html> for details of the AQS API.

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3.18 score 1 dependents 7 scripts 198 downloads

pargasite - Pollution-Associated Risk Geospatial Analysis Site

Offers tools to estimate and visualize levels of major pollutants (CO, NO2, SO2, Ozone, PM2.5 and PM10) across the conterminous United States for user-defined time ranges. Provides functions to retrieve pollutant data from the U.S. Environmental Protection Agency’s 'Air Quality System' (AQS) API service <https://aqs.epa.gov/aqsweb/documents/data_api.html> for interactive visualization through a 'shiny' application, allowing users to explore pollutant levels for a given location over time relative to the National Ambient Air Quality Standards (NAAQS).

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2.70 score 7 scripts 678 downloads

LCMSQA - Liquid Chromatography/Mass Spectrometry (LC/MS) Quality Assessment

The goal of 'LCMSQA' is to make it easy to check the quality of liquid chromatograph/mass spectrometry (LC/MS) experiments using a 'shiny' application. This package provides interactive data visualizations for quality control (QC) samples, including total ion current chromatogram (TIC), base peak chromatogram (BPC), mass spectrum, extracted ion chromatogram (XIC), and feature detection results from internal standards or known metabolites.

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2.70 score 2 scripts 207 downloads