• BioHMM

  • Referenced in 13 articles [sw10920]
  • method (BioHMM) for segmenting array comparative genomic hybridization data into states with the same underlying...
  • CNV-seq

  • Referenced in 11 articles [sw17970]
  • important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used...
  • CGH-Plotter

  • Referenced in 9 articles [sw07372]
  • with a graphical user interface for comparative genomic hybridization (CGH) data analysis. The CGH-Plotter...
  • curvclust

  • Referenced in 6 articles [sw07435]
  • functional data analysis on microarray comparative genomic hybridization (CGH) data. Our procedure is available through...
  • CGHclassify

  • Referenced in 4 articles [sw17253]
  • Array-based comparative genomic hybridization (aCGH). aCGH Clone Classification R Software...
  • cghseg

  • Referenced in 4 articles [sw06783]
  • profiles The statistical analysis of array comparative genomic hybridization (CGH) data has now shifted...
  • FLLat

  • Referenced in 2 articles [sw19127]
  • multi-sample aCGH data. Array-based comparative genomic hybridization (aCGH) enables the measurement...
  • CGHMultiArray

  • Referenced in 1 article [sw35534]
  • exact P-values for multi-array comparative genomic hybridization data. We compute P-values, based ... compare two conditions with array comparative genomic hybridization data, and we provide a simple interface...
  • CGHnormaliter

  • Referenced in 1 article [sw19117]
  • aberrations. Normalization and centralization of array comparative genomic hybridization (aCGH) data. The algorithm uses...
  • CGH-Explorer

  • Referenced in 1 article [sw35543]
  • statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing...
  • Acgh.spline

  • Referenced in 1 article [sw18847]
  • careful normalization of array-based comparative genomic hybridization (aCGH) data is of critical importance...
  • HyDe

  • Referenced in 2 articles [sw29663]
  • hybridization detection use simple site pattern frequencies from observed genomic data and compare them ... flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits...
  • Circos

  • Referenced in 4 articles [sw27740]
  • Circos: an information aesthetic for comparative genomics. We created a visualization tool called Circos ... comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally ... relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome...
  • SLAM

  • Referenced in 5 articles [sw17327]
  • with a generalized pair hidden Markov model. Comparative-based gene recognition is driven ... gene structure and alignment of two syntenic genomic regions. A key feature of the method ... generalized pair hidden Markov model, a hybrid of (1) generalized hidden Markov models, which have ... most notably with fewer false-positive predictions compared to previous methods (examples are provided...
  • RNAplex

  • Referenced in 4 articles [sw17143]
  • RNAcofold and RNAup are too slow for genome-wide search. Tools like RNAhybrid that neglects ... RNAplex, especially designed to quickly find possible hybridization sites for a query RNA in large ... computational time by a factor 10–27 compared to RNAhybrid. In addition a length penalty...
  • CISA

  • Referenced in 1 article [sw16993]
  • genomes. A tool, named CISA, has been developed to integrate the assemblies into a hybrid ... assemblies of superior contiguity and accuracy, compared with the assemblies generated by the state...
  • Phylo-MCOA

  • Referenced in 2 articles [sw18727]
  • hybridization, and horizontal gene transfers. Here, we propose a new method to explore the genomic ... inertia analysis (MCOA), which efficiently captures and compares the similarities in the phylogenetic topologies produced...
  • CorrT

  • Referenced in 1 article [sw26432]
  • zero. A natural example is a genome-wide gene expression profiling, where all genes ... variety of frameworks: sparse, non-sparse and hybrid models where sparse and dense signals ... favorable performance of the CorrT test compared to the state-of-the-art methods...
  • CRHunter

  • Referenced in 0 articles [sw25090]
  • homological relationships become weak. Nevertheless, the hybrid algorithm CRHunter consistently achieves optimal performance among ... enzymes. Compared with state-of-the-art methods, CRHunter yields comparable or better performance ... application of this algorithm to structural genomics targets sheds light on solved protein structures with...
  • LAPACK

  • Referenced in 1626 articles [sw00503]
  • LAPACK is written in Fortran 90 and provides...