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bioc
GWASTools:Tools for Genome Wide Association Studies
Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.
Maintained by Stephanie M. Gogarten. Last updated 14 days ago.
snpgeneticvariabilityqualitycontrolmicroarray
17 stars 10.67 score 396 scripts 5 dependentsbioc
GENESIS:GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
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.
Maintained by Stephanie M. Gogarten. Last updated 2 months ago.
snpgeneticvariabilitygeneticsstatisticalmethoddimensionreductionprincipalcomponentgenomewideassociationqualitycontrolbiocviews
36 stars 10.44 score 342 scripts 1 dependentsbioc
gwasurvivr:gwasurvivr: an R package for genome wide survival analysis
gwasurvivr is a package to perform survival analysis using Cox proportional hazard models on imputed genetic data.
Maintained by Abbas Rizvi. Last updated 5 months ago.
genomewideassociationsurvivalregressiongeneticssnpgeneticvariabilitypharmacogenomicsbiomedicalinformatics
12 stars 6.43 score 75 scriptsbioc
RAIDS:Accurate Inference of Genetic Ancestry from Cancer Sequences
This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.
Maintained by Pascal Belleau. Last updated 5 months ago.
geneticssoftwaresequencingwholegenomeprincipalcomponentgeneticvariabilitydimensionreductionbiocviewsancestrycancer-genomicsexome-sequencinggenomicsinferencer-languagerna-seqrna-sequencingwhole-genome-sequencing
5 stars 6.23 score 19 scripts
thomaschln
snplinkage:Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations
Linkage disequilibrium visualizations of up to several hundreds of single nucleotide polymorphisms (SNPs), annotated with chromosomic positions and gene names. Two types of plots are available for small numbers of SNPs (<40) and for large numbers (tested up to 500). Both can be extended by combining other ggplots, e.g. association studies results, and functions enable to directly visualize the effect of SNP selection methods, as minor allele frequency filtering and TagSNP selection, with a second correlation heatmap. The SNPs correlations are computed on Genotype Data objects from the 'GWASTools' package using the 'SNPRelate' package, and the plots are customizable 'ggplot2' and 'gtable' objects and are annotated using the 'biomaRt' package. Usage is detailed in the vignette with example data and results from up to 500 SNPs of 1,200 scans are in Charlon T. (2019) <doi:10.13097/archive-ouverte/unige:161795>.
Maintained by Thomas Charlon. Last updated 4 months ago.
geneticvariabilitymicroarraysnp
4.62 score 14 scriptsbioc
SIM:Integrated Analysis on two human genomic datasets
Finds associations between two human genomic datasets.
Maintained by Renee X. de Menezes. Last updated 5 months ago.
4.30 score 3 scriptsbioc
mBPCR:Bayesian Piecewise Constant Regression for DNA copy number estimation
It contains functions for estimating the DNA copy number profile using mBPCR with the aim of detecting regions with copy number changes.
Maintained by P.M.V. Rancoita. Last updated 5 months ago.
acghsnpmicroarraycopynumbervariation
3.90 score 1 scripts