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r-ggbio
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The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.
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2025-03-25 |
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r-finemapr
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public |
R wrapper to fine-mappers.
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2025-03-25 |
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r-gwasglue
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Many tools exist that use GWAS summary data for colocalisation, fine mapping, Mendelian randomization, visualisation, etc. This package is a conduit that connects R packages that can retrieve GWAS summary data to various tools for analysing those data.
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2025-03-25 |
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r-twosamplemr
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A package for performing Mendelian randomization using GWAS summary data. It uses the IEU GWAS database to obtain data automatically, and a wide range of methods to run the analysis. You can use the MR-Base web app to try out a limited range of the functionality in this package, but for any serious work we strongly recommend using this R package.
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2025-03-25 |
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r-gwasvcf
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public |
Tools for dealing with GWAS summary data in VCF format. Includes reading, querying, writing, as well as helper functions such as LD proxy searches.
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2025-03-25 |
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r-mrpresso
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MR-PRESSO (Mendelian Randomization Pleiotropy RESidual Sum and Outlier) is a framework that allows for the evaluation of pleiotropy in multi-instrument Mendelian Randomization utilizing genome-wide summary association statistics.
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2025-03-25 |
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r-radialmr
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A package for implementing radial inverse variance weighted and MR-Egger methods.
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2025-03-25 |
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r-ieugwasr
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R interface to the IEU GWAS database API. Includes a wrapper to make generic calls to the API, plus convenience functions for specific queries.
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2025-03-25 |
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r-genetics.binaries
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public |
Convenient way to make binaries such as plink, bcftools etc available to other packages
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2025-03-25 |
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pcangsd
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public |
Framework for analyzing low depth NGS data in heterogeneous populations using PCA
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2025-03-25 |
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r-mendelianrandomization
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Encodes several methods for performing Mendelian randomization analyses with summarized data. Summarized data on genetic associations with the exposure and with the outcome can be obtained from large consortia. These data can be used for obtaining causal estimates using instrumental variable methods.
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2025-03-25 |
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r-coloc
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Performs the colocalisation tests described in Plagnol et al (2009) <doi:10.1093/biostatistics/kxn039>, Wallace et al (2013) <doi:10.1002/gepi.21765>, Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>, Wallace (2020) <doi:doi.org/10.1371/journal.pgen.1008720>.
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2025-03-25 |
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r-racer
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In order to investigate and compare regional association data, one may need to create a single plot of a regional association, a scatter plot of the -log10(p-values)s of two studies, or a mirror plot, a plot comparing two sets of -log10(p-value)s that are mirrored across a common x-axis. RACER can be used to create these three types of plots. This package is described further in Sabik and Farber (2018) <doi:10.1101/495366>.
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2025-03-25 |
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r-fst
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Multithreaded serialization of compressed data frames using the 'fst' format. The 'fst' format allows for random access of stored data and compression with the LZ4 and ZSTD compressors created by Yann Collet. The ZSTD compression library is owned by Facebook Inc.
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2025-03-25 |
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r-snprelate
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Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package SNPRelate to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 classes and generic functions. The extended GDS format is implemented in the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls.
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2025-03-25 |
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r-genesis
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The GENESIS package provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides functions to perform PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components Analysis on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. Unlike standard PCA, PC-AiR accounts for relatedness in the sample to provide accurate ancestry inference that is not confounded by family structure. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry and accurately estimate measures of recent genetic relatedness such as kinship coefficients, IBD sharing probabilities, and inbreeding coefficients. Additionally, functions are provided to perform efficient variance component estimation and mixed model association testing for both quantitative and binary phenotypes.
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2025-03-25 |
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r-openmpcontroller
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The OpenMPController package provides a function omp_set_num_threads() to set the number of OpenMP threads to be used. This may be useful, for example, when linking against a vendor optimised BLAS/LAPACK library (e.g. the AMD Core Math Library), since the defaults used by those libraries may not be highly performant.
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2025-03-25 |
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r-lme4qtl
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Linear mixed models (lme4) with flexible covariance structure for qtl and association analysis.
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2025-03-25 |
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r-cause
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public |
Identify causal patterns using pairs of GWAS summary statistics.
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2025-03-25 |
