• MethylSig

  • Referenced in 4 articles [sw23506]
  • sequences. The wide application of reduced representation bisulfite sequencing (RRBS) and whole genome bisulfite sequencing ... statistical analysis package, methylSig, to analyse genome-wide methylation differences between samples from different treatments...
  • GWAF

  • Referenced in 1 article [sw19000]
  • GWAF: an R package for genome-wide association analyses with family data. Summary: GWAF, Genome...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • cell simulation. MOTIVATION: Genome sequencing projects and further systematic functional analyses of complete gene sets ... unprecedented mass of molecular information for a wide range of model organisms. This provides ... smallest known chromosome, whose complete 580 kb genome sequence was determined at TIGR...
  • COBRA Toolbox

  • Referenced in 13 articles [sw32083]
  • widely used for modelling, analysing and predicting a variety of metabolic phenotypes using genome-scale...
  • CNVassoc

  • Referenced in 2 articles [sw19389]
  • order to make feasible the analyses of Genome Wide Association studies (GWAs) with hundreds...
  • pi-MASS

  • Referenced in 20 articles [sw17249]
  • issue of “missing heritability” in genome-wide association studies. More generally, we demonstrate that, despite ... predictive performance compared with standard single-SNP analyses and the penalized regression method LASSO. Methods...
  • MaCH

  • Referenced in 7 articles [sw17274]
  • estimate haplotypes and unobserved genotypes. Genome-wide association studies (GWAS) can identify common alleles that ... widely used to facilitate comparison of results across studies as well as meta-analyses ... genotype imputation not only facilitates cross study analyses but also increases power of genetic association ... reference is very accurate using either genome-wide SNP data or smaller amounts of data...
  • GW-SEM

  • Referenced in 1 article [sw37731]
  • been integrated into standard genome-wide association analyses because fitting a SEM at each single ... nucleotide polymorphism (SNP) along the genome was hitherto considered to be too computationally demanding ... enormous amount of data that genome-wide scans produce, the statistical methods used to analyze ... latent construct on a genome-wide basis using a Diagonally Weighted Least Squares (DWLS) estimator...
  • r2VIM

  • Referenced in 1 article [sw27009]
  • Selection Method for Random Forests in Genome-Wide Association Studies. Machine learning methods ... alternative to standard single SNP analyses in genome-wide association studies (GWAS). RFs provide variable ... many SNPs should be selected for downstream analyses (i.e. for feature selection while controlling false...
  • GoSurfer

  • Referenced in 2 articles [sw35672]
  • gene sets obtained from genome-wide computations or microarray analyses. GoSurfer is a graphical interactive...
  • MetaGeneAnnotator

  • Referenced in 3 articles [sw17338]
  • expedite wide ranges of microbial genome studies, such as genome annotations and metagenome analyses...
  • SlideSort

  • Referenced in 1 article [sw28786]
  • novo genome assembly, genome-wide alignment and other important analyses. Results: In this study...
  • PIPE

  • Referenced in 6 articles [sw26869]
  • vid30c. Also, PIPE can be used to analyse yeast proteins for which TAP tagging fails ... interactions that are not included in genome-wide yeast TAP tagging projects. Conclusion: PIPE analysis...
  • Notung

  • Referenced in 13 articles [sw08917]
  • genetic functional innovation. Whole genome duplications are widely believed to have played an important role ... evolution of the maize, yeast, and vertebrate genomes. The use of evolutionary trees to analyze ... this approach on small data sets, using analyses performed by hand. The rapid growth...
  • snpQC

  • Referenced in 1 article [sw17243]
  • Illumina SNP genotyping array data. In genome-wide association studies, quality control (QC) of genotypes ... perform QC analyses of Illumina SNP array data. It applies a wide range of common ... dataset, including a genomic relationship matrix, ready for further downstream analyses which make it amenable ... between the genotyping laboratory and downstream genome-wide association study or genomic prediction...
  • BayesPeak

  • Referenced in 8 articles [sw18843]
  • package for analysing chip-seq data. Motivation: Identification of genomic regions of interest in ChIP ... genome implementation. Results: In this note we present BayesPeak, an R package for genome-wide...
  • FUNC

  • Referenced in 2 articles [sw16930]
  • gene sets and ontological annotations. Background: Genome-wide expression, sequence and association studies typically yield ... gene candidates, which must then be further analysed and interpreted. Information about these genes ... assess the statistical significance of such analyses since many inter-dependent categories are tested simultaneously ... tests in particular well suited for genome wide sequence comparisons, estimates of the family-wise...
  • dartR

  • Referenced in 1 article [sw38558]
  • dartR: Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis...
  • TreeFix

  • Referenced in 6 articles [sw29607]
  • clades of 12 Drosophila and 16 fungal genomes, as well as to simulated phylogenies ... should be applicable to a wide range of analyses and have many important implications...
  • TATES

  • Referenced in 3 articles [sw20044]
  • wide association studies. To date, the genome-wide association study (GWAS) is the primary tool ... variants that cause phenotypic variation. As GWAS analyses are generally univariate in nature, multivariate phenotypic...