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r-intsurv
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public |
Contains implementations of integrative survival analysis routines, including regular Cox cure rate model proposed by Kuk and Chen (1992) <doi:10.1093/biomet/79.3.531> via an EM algorithm proposed by Sy and Taylor (2000) <doi:10.1111/j.0006-341X.2000.00227.x>, regularized Cox cure rate model with elastic net penalty following Masud et al. (2018) <doi:10.1177/0962280216677748>, and Zou and Hastie (2005) <doi:10.1111/j.1467-9868.2005.00503.x>, and weighted concordance index for cure models proposed by Asano and Hirakawa (2017) <doi:10.1080/10543406.2017.1293082>.
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2025-03-25 |
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r-ivtools
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public |
Contains tools for instrumental variables estimation. Currently, non-parametric bounds, two-stage estimation and G-estimation are implemented. Balke, A. and Pearl, J. (1997) <doi:10.2307/2965583>, Vansteelandt S., Bowden J., Babanezhad M., Goetghebeur E. (2011) <doi:10.1214/11-STS360>.
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2025-03-25 |
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r-ahaz
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Computationally efficient procedures for regularized estimation with the semiparametric additive hazards regression model.
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2025-03-25 |
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r-easypubmed
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public |
Query NCBI Entrez and retrieve PubMed records in XML or text format. Process PubMed records by extracting and aggregating data from selected fields. A large number of records can be easily downloaded via this simple-to-use interface to the NCBI PubMed API.
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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 |
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r-mixie
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public |
Permorm mixIE methods including mixIE-MA and mixIE-MA-DP.
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2025-03-25 |
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r-gwasglue
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public |
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-finemapr
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R wrapper to fine-mappers.
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2025-03-25 |
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r-gwasvcf
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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-genetics.binaries
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public |
A convenient way to make binaries such as plink, bcftools, and others available to other packages. This package forms part of the MRC IEU OpenGWAS system. The system includes other R packages, including; gwasglue, ieugwasr, gwasvcf, and TwoSampleMR.
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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-mr.raps
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Mendelian randomization is a method of identifying and estimating a confounded causal effect using genetic instrumental variables. This packages implements methods for two-sample Mendelian randomization with summary statistics by using Robust Adjusted Profile Score (RAPS). References: Qingyuan Zhao, Jingshu Wang, Jack Bowden, Dylan S. Small. Statistical inference in two-sample summary-data Mendelian randomization using robust adjusted profile score. <arXiv:1801.09652>.
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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-mrmix
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This package gives robust estimation of causal effects by conducting Mendelian randomization analysis using a mixture model approach.
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2025-03-25 |
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r-mrpresso
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public |
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-mrinstruments
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Datasets of eQTLs, GWAS catalogs, etc
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2025-03-25 |
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r-mendelianrandomization
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public |
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-mia
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public |
mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.
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2025-03-25 |
