• PMA

  • Referenced in 74 articles [sw19126]
  • package PMA: Penalized Multivariate Analysis. Performs Penalized Multivariate Analysis: a penalized matrix decomposition, sparse principal ... components analysis, and sparse canonical correlation analysis, described in the following papers: (1) Witten, Tibshirani ... sparse principal components and canonical correlation analysis. Biostatistics 10(3):515-534. (2) Witten ... canonical correlation analysis, with applications to genomic data. Statistical Applications in Genetics and Molecular Biology...
  • gap

  • Referenced in 2 articles [sw24918]
  • Genetic Analysis Package. It is designed as an integrated package for genetic data analysis...
  • Arlequin

  • Referenced in 4 articles [sw11442]
  • integrated software package for population genetics data analysis. Arlequin ver 3.0 is a software package ... several basic and advanced methods for population genetics data analysis, like the computation of standard...
  • GENEHUNTER

  • Referenced in 1 article [sw18773]
  • methodology is based around the genetic analysis package GENEHUNTER. However, the approach can be adapted...
  • Haploview

  • Referenced in 19 articles [sw11870]
  • Haploview: analysis and visualization of LD and haplotype maps. Research over the last few years ... genetic association studies, is becoming a routine research activity. Haploview is a software package that...
  • adegenet

  • Referenced in 3 articles [sw07121]
  • adegenet: adegenet: an R package for the exploratory analysis of genetic and genomic data Classes...
  • Pegas

  • Referenced in 1 article [sw19001]
  • pegas (Population and Evolutionary Genetics Analysis System) is a new package for the analysis ... existing R packages (ape and adegenet). pegas provides functions for standard population genetic methods ... modular approach for software dedicated to the analysis of population genetic data. Availability: pegas...
  • MENDEL

  • Referenced in 6 articles [sw14990]
  • genetic analysis programs. Summary: Mendel is one of the few statistical genetics packages that provide...
  • ProbABEL

  • Referenced in 6 articles [sw10861]
  • hazards models, respectively. For quantitative traits, the package also implements a fast two-step mixed ... relationships, facilitating analysis in family-based studies, studies performed in human genetically isolated populations ... outbred animal populations. Conclusions: ProbABEL package provides fast efficient way to analyze imputed data...
  • HyPhy

  • Referenced in 2 articles [sw23146]
  • open-source software package for the analysis of genetic sequences (in particular the inference...
  • Polyunphased

  • Referenced in 1 article [sw19781]
  • outcomes of the unphased package for family-based genetic association analysis. Polytomous phenotypes arise when ... conditional polytomous logistic regression for within-family analysis robust to population stratification. We introduce Polyunphased ... Unphased package, a flexible software tool for genetic association analysis in nuclear families. Like Unphased...
  • sva

  • Referenced in 3 articles [sw21306]
  • package SVA: Surrogate Variable Analysis. The sva package contains functions for removing batch effects ... high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate ... latent sources of noise. The sva package can be used to remove artifacts in three ... throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch...
  • MAPMAKER

  • Referenced in 5 articles [sw18435]
  • MAPMAKER: an interactive computer package for constructing primary genetic linkage maps for experimental and natural ... populations. With the advent of RFLPs, genetic linkage maps are now being assembled ... Accurate construction of such genetic maps requires multipoint linkage analysis of particular types of pedigrees ... describe here a computer package, called MAPMAKER, designed specifically for this purpose. The program uses...
  • GeneticTools

  • Referenced in 1 article [sw24178]
  • package GeneticTools: Collection of Genetic Data Analysis Tools. GeneticTools is a loose collection of tools...
  • onemap

  • Referenced in 3 articles [sw20322]
  • package onemap: Software for constructing genetic maps in experimental crosses: full-sib, RILs ... backcrosses. Analysis of molecular marker data from model (backcrosses, F2 and recombinant inbred lines...
  • SPAGEDi

  • Referenced in 2 articles [sw07534]
  • SPAGeDi (Spatial Pattern Analysis of Genetic Diversity) is a computer package primarily designed to characterise ... similar to a spatial autocorrelation analysis, 2°) by linear regressions (the slopes of these regressions...
  • SyMod

  • Referenced in 1 article [sw13046]
  • promise for solving complex problems in human genetics. Unfortunately, many of these methods ... their ready adoption and integration into an analysis or modeling paradigm that might otherwise only ... source, platform-independent, and freely-available software packages that are designed to be used ... comprehensive software package that puts powerful GP methods for genetic analysis in the hands...
  • CGEN

  • Referenced in 1 article [sw14737]
  • CGEN: An R package for analysis of case-control studies in genetic epidemiology...
  • PGEToolbox

  • Referenced in 1 article [sw12455]
  • Toolbox for Population Genetics and Evolution. Assessing genetic diversity within populations is vital for understanding ... based open-sourced software package for data analysis in population genetics. The main features...
  • BiGG

  • Referenced in 7 articles [sw17247]
  • describe BiGG, a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions ... models for further analysis by external software packages. Users may follow links from BiGG...