• BEDTools

  • Referenced in 11 articles [sw17302]
  • genomics research. However, searching for overlaps between features with existing web-based methods is complicated...
  • Tabix

  • Referenced in 3 articles [sw28170]
  • export, and quickly retrieves features overlapping specified regions. Tabix features include few seek function calls...
  • PISA

  • Referenced in 2 articles [sw27597]
  • pixel and makes use of densely overlapping, feature-adaptive observations for saliency measure computation...
  • ARACHNE

  • Referenced in 9 articles [sw07552]
  • several key features, including an efficient and sensitive procedure for finding read overlaps, a procedure...
  • propOverlap

  • Referenced in 1 article [sw33153]
  • package propOverlap: Feature (gene) selection based on the Proportional Overlapping Scores. A package for selecting ... classification problems. The discriminative features are identified using analyzing the overlap between the expression values ... defined in the ”Proportional Overlapping Score (POS)” technique for feature selection. A gene mask which...
  • POIMs

  • Referenced in 2 articles [sw35360]
  • correlation structure of k-mer features induced by overlaps of related k-mers into account...
  • CAP3

  • Referenced in 16 articles [sw08935]
  • includes a number of improvements and new features. The program has a capability to clip ... uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments...
  • PuFFIN

  • Referenced in 2 articles [sw22390]
  • overlapping nucleosomes without any user-defined parameter. This feature makes PuFFIN significantly easier ... produces a consensus set that satisfies non-overlapping constraints and maximizes the number of nucleosomes...
  • CA

  • Referenced in 1 article [sw26440]
  • solution are also introduced. Some of the features of the package include colored graphics, incremental ... determine identities of overlapping points, and stability and fit measures. The features of the package...
  • RNA2D3D

  • Referenced in 1 article [sw17141]
  • content, it features efficient interactive graphical editing for the removal of any overlaps introduced ... making conformational changes favorable to targeted features and subsequent refinement. With emphasis on fast exploration...
  • margrave

  • Referenced in 2 articles [sw28803]
  • powerful features for firewall analysis, including enumerating consequences of configuration edits, detecting overlaps and conflicts...
  • MDCGen

  • Referenced in 1 article [sw32196]
  • implements classic pursued features: (a) customization of cluster-separation, (b) overlap control, (c) addition...
  • RPEnsemble

  • Referenced in 2 articles [sw16698]
  • feature vectors into a lower-dimensional space. The random projections are divided into non-overlapping...
  • GeneSigDB

  • Referenced in 4 articles [sw17287]
  • browse function, facetted navigation and a ‘basket’ feature to store genes or gene signatures ... identify gene signatures with significant gene overlap and results can be viewed on a dynamic...
  • CpGcluster

  • Referenced in 4 articles [sw35410]
  • Phylogenetic Conserved Elements (PhastCons). CpGcluster’s CGIs overlapping with the Transcription Start Site (TSS) show ... significant clusters of CpG dinucleotides. Another outstanding feature is that all predicted CGIs start ... which should be appropriate for a genomic feature whose functionality is based precisely ... lead to the high specificity and low overlap with spurious Alu elements observed for CpGcluster...
  • PCAP

  • Referenced in 3 articles [sw17185]
  • reads. The PCAP program has several features to address efficiency and accuracy issues in assembly ... sensitive method is used to avoid missing overlaps caused by sequencing errors. Repetitive regions...
  • Valmet

  • Referenced in 9 articles [sw01281]
  • validation and comparison of object segmentation. New features not available in commercial and public-domain ... four different shape distance metrics, a) percentage overlap of segmented structures (R intersect...
  • PalmPrints

  • Referenced in 2 articles [sw01755]
  • evolutionary clustering algorithm with dynamic clustering and feature selection; (b) an extended fitness function, which ... average clustering of 4 clusters, with minimal overlap between them...
  • ROSITA

  • Referenced in 1 article [sw13296]
  • complete vertical axis wind turbine using overlapping grids. Three-dimensional simulations of the aerodynamic field ... comparison to experimental data confirms the general features of the flow...
  • seg1d

  • Referenced in 1 article [sw34992]
  • parameters for the process through weighted features (i.e., additional data attributed to the same ... algorithm finds the most prominent segments. Non-overlapping segments are identified and a clustering algorithm...