• pi-MASS

  • Referenced in 17 articles [sw17249]
  • identify regions harboring SNPs that affect some phenotype or outcome of interest. This goal ... methods. We focus primarily on analysis of quantitative phenotypes, and on appropriate prior specification...
  • CellProfiler

  • Referenced in 17 articles [sw18751]
  • CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Biologists can now prepare ... designed for flexible, high-throughput cell image analysis, CellProfiler. CellProfiler can address a variety...
  • TATES

  • Referenced in 3 articles [sw20044]
  • TATES: efficient multivariate genotype-phenotype analysis for genome-wide association studies. To date, the genome ... tool to identify genetic variants that cause phenotypic variation. As GWAS analyses are generally univariate...
  • Eigenstrat

  • Referenced in 56 articles [sw33845]
  • EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls ... supports multiple file formats and quantitative phenotypes...
  • BioSig

  • Referenced in 2 articles [sw35770]
  • BioSig: an imaging bioinformatics system for phenotypic analysis. Organisms express their genomes in a cell ... manner, resulting in a variety of cellular phenotypes or phenomes. Mapping cell phenomes under...
  • edgeR

  • Referenced in 53 articles [sw06936]
  • genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves ... levels of replication, provided at least one phenotype or experimental condition is replicated. The software...
  • COBRA Toolbox

  • Referenced in 13 articles [sw32083]
  • well as biased and unbiased model-driven analysis methods. It is widely used for modelling ... analysing and predicting a variety of metabolic phenotypes using genome-scale biochemical networks...
  • GW-SEM

  • Referenced in 1 article [sw37731]
  • Modeling (SEM), are valuable in the phenotypic analysis of psychiatric and substance use phenotypes...
  • MASTOR

  • Referenced in 2 articles [sw23134]
  • some individuals to have missing data (phenotypes, genotypes, or covariates). When some individuals ... gained by incorporating all individuals in the analysis, including individuals with partially missing data, while ... data in the analysis while correcting for dependence. Individuals with available phenotype and covariate information ... missing covariate or phenotype information can contribute to the analysis. MASTOR is valid even when...
  • Ebimage

  • Referenced in 12 articles [sw18998]
  • cellular phenotypes. EBImage provides general purpose functionality for reading, writing, processing and analysis of images...
  • SNPeffect

  • Referenced in 2 articles [sw30038]
  • protein-coding SNVs on the structural phenotype of proteins. It integrates aggregation prediction (TANGO), amyloid ... prediction (LIMBO) and protein stability analysis (FoldX) for structural phenotyping. Additionally, SNPeffect holds information ... submit custom protein variants for a SNPeffect analysis, including automated structure ... modeling. The new meta-analysis application allows plotting correlations between phenotypic features for a user...
  • PBAT

  • Referenced in 6 articles [sw10529]
  • analysis, FBAT-PC amplifies the genetic effects of each measurement by constructing an overall phenotype ... overall phenotype and the power of FBAT-PC. Compared to univariate analysis, FBAT-PC achieves...
  • HPOSim

  • Referenced in 1 article [sw16935]
  • Package for Phenotypic Similarity Measure and Enrichment Analysis Based on the Human Phenotype Ontology. Background ... comprehensive resource for computational analysis of human disease phenotypes. Most of the existing HPO-based ... HPOSim is an R package for analyzing phenotypic similarity for genes and diseases based ... similarity measures are implemented in HPOSim. Enrichment analysis of gene sets and disease sets...
  • Polyunphased

  • Referenced in 1 article [sw19781]
  • package for family-based genetic association analysis. Polytomous phenotypes arise when a disease has multiple ... family analysis robust to population stratification. We introduce Polyunphased, an extension to polytomous phenotypes ... flexible software tool for genetic association analysis in nuclear families. Like Unphased, Polyunphased is written ... former approach is thus recommended with polytomous phenotypes...
  • SIMLA

  • Referenced in 5 articles [sw00862]
  • which can be used to generate disease phenotype and marker genotype data in three-generational ... different linkage and association analysis methods applied to complex human phenotypes. SIMLA can assist investigators...
  • ShapePheno

  • Referenced in 1 article [sw14414]
  • major bottleneck. Automatic image analysis is one major strategy to phenotype individuals in large numbers ... deformation phenotypes from biological images, making them available as quantitative traits for downstream analysis ... reticulata). We find that the flexible shape phenotypes our model extracts are complementary to basic...
  • QSSPN

  • Referenced in 1 article [sw30010]
  • will enable the mechanistic prediction of genotype–phenotype relationships. Despite advances in quantitative biology, full ... method integrating Petri nets and constraint-based analysis to predict the feasibility of qualitative dynamic ... dynamic behaviours and permit mechanistic analysis of genotype–phenotype relationships. Availability and implementation: The model...
  • ZFIQ

  • Referenced in 1 article [sw30480]
  • relationship between genotype and phenotype, for pathway analysis and systems biology. However, the tremendous amount...
  • recount

  • Referenced in 10 articles [sw17315]
  • ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. Explore ... exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample ... different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation...
  • BayesTwin

  • Referenced in 1 article [sw27257]
  • measurement model is estimated, allowing analysis of the raw phenotypic (item-level) data. The integration ... since earlier research has shown that an analysis based on an aggregated measure...