Categories
Tag: SNPRelate
Bioconductor Code: SNPRelate
SNPRelate: Parallel computing toolset for relatedness and principal component analysis of SNP data ==== ![GPLv3](http://www.gnu.org/graphics/gplv3-88×31.png) [GNU General Public License, GPLv3](http://www.gnu.org/copyleft/gpl.html) [![Availability](http://www.bioconductor.org/shields/availability/release/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![Years-in-BioC](http://www.bioconductor.org/shields/years-in-bioc/SNPRelate.svg)](http://www.bioconductor.org/packages/release/bioc/html/SNPRelate.html) [![R](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml/badge.svg)](https://github.com/zhengxwen/SNPRelate/actions/workflows/r.yml) ## Features Genome-wide association studies are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed SNPRelate (R…
Saving the output of LD pruning from SNPRelate package as a new GDS file
Saving the output of LD pruning from SNPRelate package as a new GDS file 1 I successfully ran LD pruning from SNPRelate package and obtained the selected SNPs IDs. I would like to create a new GDS file with only the pruned SNPs so I can use it in another…
Bioconductor – VariantExperiment
DOI: 10.18129/B9.bioc.VariantExperiment This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see VariantExperiment. A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend Bioconductor version: 3.12 VariantExperiment is a Bioconductor package for saving data in VCF/GDS format into RangedSummarizedExperiment object. The high-throughput genetic/genomic data…
Bioconductor – gdsfmt
DOI: 10.18129/B9.bioc.gdsfmt This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see gdsfmt. R Interface to CoreArray Genomic Data Structure (GDS) Files Bioconductor version: 3.15 Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms…
Bioconductor – SeqArray
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see SeqArray. Big Data Management of Whole-genome Sequence Variant Calls Bioconductor version: 3.4 Big data management of whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls)…
Help with PCA plot from SNPRelate
Hello, BioStars community! I am working on a datase of 50 samples(between cases and controls) with genotyping data for ~200 SNPs. I ran SNPRelate PCA analysis without adding population data and tried to plot its results. My PCA plot seems a bit “strange” since the observations did not come together…
Bioconductor – SNPRelate
DOI: 10.18129/B9.bioc.SNPRelate This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SNPRelate. Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data Bioconductor version: 3.12 Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and…
Index of /contrib/main/00Archive/SNPRelate
Name Last modified Size Description Parent Directory – SNPRelate_0.9.0.tar.gz 2011-08-03 06:26 3.1M SNPRelate_0.9.1.tar.gz 2011-08-13 13:04 3.1M SNPRelate_0.9.2.tar.gz 2012-02-02 07:30 1.1M SNPRelate_0.9.3.tar.gz 2012-03-05 07:20 1.1M SNPRelate_0.9.4.tar.gz 2012-03-17 09:18 1.1M SNPRelate_0.9.5.tar.gz 2012-04-25 04:39 1.1M SNPRelate_0.9.6.tar.gz 2012-07-22 06:19 1.5M SNPRelate_0.9.7.tar.gz 2012-08-30 05:14 3.0M …
PCA on pooled and single individuals
PCA on pooled and single individuals 0 Hello all, I am trying to carry out a population structure analysis using a set of samples that includes pooled and single individuals. After performing the PCA using SNPRelate, pooled individuals are clustered together, which suggests that the sample type is an averaging…