Artifacts using Gdsfmt (7)

Sort by:Popular▼

✓Popular✓Newest

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

A High-performance computing toolset for relatedness and principal component analysis of SNP data

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.

It is a software package for imputing HLA types using SNP data, and relies on a training set of HLA and SNP genotypes. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and ...

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 ...

Reliable and rapid ethnicity annotation from whole exome sequencing data.

Processing pipeline for 'SamBada' from pre- to post-processing. 'SamBada' is a landscape genomic software designed to run univariate or multivariate logistic regression between the presence of a genotype and one or several environmental variables. See Stucki (2017) <doi:10.1111/1755-0998.12629> and <https://github.com/Sylvie/sambada>. The package provides functions that can be classified into four categories: 1) Install 'SamBada' 2) Preprocessing (prepare genomic file into standards compatible with ...