• JIVE

  • Referenced in 14 articles [sw09511]
  • data types, low-rank approximations for structured variation individual to each data type, and residual ... noise. JIVE quantifies the amount of joint variation between data types, reduces the dimensionality ... visual exploration of joint and individual structures. The proposed method represents an extension of Principal...
  • PhyloWGS

  • Referenced in 6 articles [sw26926]
  • point mutations and population frequencies of structural variations. We introduce a principled phylogenic correction...
  • ProDy

  • Referenced in 4 articles [sw24072]
  • ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved ... these variations with the theoretically predicted equilibrium dynamics. Datasets include structural ensembles for a given...
  • t-SNE

  • Referenced in 116 articles [sw22300]
  • three-dimensional map. The technique is a variation of Stochastic Neighbor Embedding (Hinton and Roweis ... creating a single map that reveals structure at many different scales. This is particularly important...
  • Pindel

  • Referenced in 4 articles [sw33143]
  • difficult and identification of long structural variations is extremely challenging. Results: We present Pindel...
  • GASV

  • Referenced in 2 articles [sw34276]
  • software packages for analysis of structural variation from paired-end sequencing and/or array-CGH data ... been tested used to find structural variation in both normal and cancer genomes using data ... platforms. It can be used to predict structural variants directly from aligned reads in SAM/BAM ... probabilistic model two common signals of structural variation. When multiple alignments of a read...
  • fastSTRUCTURE

  • Referenced in 4 articles [sw25207]
  • fastSTRUCTURE: variational inference of population structure in large SNP data sets. Tools for estimating population ... model underlying the STRUCTURE program using a variational Bayesian framework. Variational methods pose the problem ... detect weak population structure in the data. We test the variational algorithms on simulated data ... Panel. The variational algorithms are almost two orders of magnitude faster than STRUCTURE and achieve...
  • LUMPY

  • Referenced in 2 articles [sw33128]
  • structural variant discovery. Comprehensive discovery of structural variation (SV) in human genomes from DNA sequencing ... framework for comprehensive studies of structural variation in heterogeneous tumor genomes. We further discuss...
  • AJIVE

  • Referenced in 2 articles [sw27867]
  • Angle-based joint and individual variation explained. Integrative analysis of disparate data blocks measured ... data structure naturally motivates the simultaneous exploration of the joint and individual variation within each ... subspaces as the principal descriptors of variation structure and the use of perturbation theory...
  • Vaquita

  • Referenced in 1 article [sw33127]
  • Vaquita: fast and accurate identification of structural variation using combined evidence. Motivation: Comprehensive identification ... structural variations (SVs) is a crucial task for studying genetic diversity and diseases. However ... fast tool for the identification of structural variations, which leverages all four types of evidence...
  • MXML

  • Referenced in 7 articles [sw03376]
  • data which can exhibit different variations in value or structure (e.g. that can exist...
  • ARSyN

  • Referenced in 2 articles [sw09280]
  • noise within the signal) and the structured variation of the ANOVA errors (the signal ... cases where there are high levels of structural noise. Software for ARSyN is freely available...
  • Circos

  • Referenced in 5 articles [sw27740]
  • tool is effective in displaying variation in genome structure and, generally, any other kind...
  • APPROXML

  • Referenced in 2 articles [sw03152]
  • structured in different ways. Variations in structure make effective search of information across multiple datasources...
  • CIRCUS

  • Referenced in 1 article [sw23099]
  • package for Circos display of structural genome variations from paired-end and mate-pair sequencing ... package called CIRCUS to analyze genomic structural variations. It generates both data and configuration files ... allows fast and versatile analysis of genomic structural variants with Circos plots for users with...
  • RNAMotifContrast

  • Referenced in 1 article [sw39987]
  • analysis of RNA properties by recognizing structural motifs, they do not provide the means ... analyzing the similarities and variations of RNA structural motif characteristics. In this method, a graph ... that the derived subfamilies possess unique structural variations while holding standard features of the families...
  • RNAG

  • Referenced in 2 articles [sw17129]
  • structure was large relative to the variation among structures within an ensemble. Availability: The Perl...
  • HLM

  • Referenced in 44 articles [sw06516]
  • fields, research data often have a hierarchical structure. That is, the individual subjects of study ... model with explanatory variables that account for variations at each level, utilizing variables specified ... research due to the prevalence of hierarchical structures in data from this field...
  • MetaSV

  • Referenced in 1 article [sw33140]
  • variant caller for next generation sequencing. Structural variations (SVs) are large genomic rearrangements that vary...
  • SplitMEM

  • Referenced in 1 article [sw30182]
  • simple single-nucleotide polymorphisms and complex structural variations far beyond what can be represented...