Search Results for "construct"
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Showing 17 open source projects for "construct"
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MPIGeneNet
Parallel tool to construct gene co-expression networks
MPIGeneNet is a parallel tool to construct gene co-expression networks using Pearson’s correlation and Random Matrix Theory (RMT). This tool takes as input a matrix with the expression values (a float value) for different genes observed from several samples. It is a parallelization of RMTGenNet tool (https://github.com/spficklin/RMTGeneNet). MPIGeneNet integrates the whole procedure of creating the in one program, which makes the tool easier to work with (the users only have to launch the application once) and avoids writing/reading from intermediate files among the modules. -
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com-hfg
java library for XML, HTML, or SVG generation + bioinformatics classes
The com.hfg (hairyfatguy.com) library is a collection of utility classes that make it easy to construct XML, HTML, XHTML, or SVG in an object-oriented way from within your Java application or webapp. It also contains other IO utilities and bioinformatics classes for phylogenetic trees, taxonomy, and multi-chain proteins. Requires JDK1.8. -
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EvidentialGene
Evidence Directed Gene Construction for Eukaryotes
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University, see http://arthropods.eugenes.org/EvidentialGene/ Construction refers to the combination of classical gene prediction, and more recent gene assembly (de-novo and genome-assisted) methods. The basic Evigene methods involve using available best-of-breed gene prediction and assembly software, combining all evidence for genes, from expressed sequences, genome assembly sequences, related species protein sequences, and any other, to annotate and score gene constructions. ... -
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MPICorMat
Parallel tool to construct correlation similarity matrices
...RMTGeneNet users can exchange this CCM module by MPICorMat, benefit from its fast computation to generate the similarity matrix, and then use the similarity matrix as input for the second module (RMM) to construct the final gene co-expression network. -
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libSBOL provides the core C/C++ interfaces and their implementation for the Synthetic Biology Open Language (SBOL). Version 2.1.1 of libSBOL provides an API to construct SBOL 2.1.0 designs and to read and write SBOL version 2.1.0 XML/RDF files.
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Matrix factorization is applied to the B-spline basis to construct an orthonormal basis. Data can be approximated by a linear combination of the orthonormal basis functions. Constraints are imposed such that the fitted function is linear at the boundary points, as in natural cubic spline.
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Maximum Common Genome Alignment (MCGA)
Pipeline for creating core genome alignments for phylogenetic analysis
Maximum Common Genome Alignment (MCGA) Tool MCGA is a bioinformatics analysis tool written in Python for generating core genome alignment for bacterial whole genome sequences which can be used to construct phylogenetic trees. -
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Gen3D
A tool for 3D genome and chromosome structural model construction
Gen3D is an application designed to determine three-dimensional genome and chromosome models. It uses chromosomal contact data to construct three-dimensional conformations. This method can generate three-dimensional chromosomal models satisfying a large portion of chromosomal contacts. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. ... -
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SplitMEM
Graphical pan-genome analysis with suffix skips
...Here we introduce a novel O(n log n) time and space algorithm called splitMEM, that directly constructs the compressed de Bruijn graph for a pan-genome of total length n. To achieve this time complexity, we augment the suffix tree with suffix skips, a new construct that allows us to traverse several suffix links in constant time, and use them to efficiently decompose maximal exact matches (MEMs) during a suffix tree traversal. -
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SOAPdenovo-Trans
A de novo transcriptome assembler.
Latest Codes on GitHub: https://github.com/aquaskyline/SOAPdenovo-Trans SOAPdenovo-Trans is a de novo transcriptome assembler inherited from the SOAPdenovo2 framework, designed for assembling transcriptome with alternative splicing and different expression level. The assembler provides a more comprehensive way to construct the full-length transcript sets compare to SOAPdenovo2. -
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Fylogenetica
Constructing level-1-networks consistent with a set of quartets
This project is an implementation of an algorithm by J. Keijsper and R. Pendavingh. The goal of the algorithm is to construct a phylogenetic level-1-network that is consistent with a given set of quartets. -
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TreeLiker
TreeLiker is a collection of fast algorithms for working with complex
...The algorithms included in TreeLiker are unique in that, in principle, they are able to search given sets of relational patterns exhaustively, thus guaranteeing that if some good pattern capturing an important feature of the problem exists, it will be found. In experiments with real-life data, the algorithms were shown to be able to construct complete non-redundant sets of patterns for chemical datasets involving several thousands of molecules as well as for comparably large datasets from genomics or proteomics. The included relational learning algorithms are tailored towards so-called tree-like features for which some otherwise very hard sub-problems (NP-hard) become tractable. -
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Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.
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A tool to construct the metabolic networks from KEGG, and compare the constructed metabolic networks. Phylogenetic trees can be constructed along the case.
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Annotare is a tool for annotating Microarray and Gene Expression data. It will help a bench biologist construct a MIAME-compliant MAGE-TAB file.
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Protege is a free, open-source platform that provides a suite of tools to construct domain models and knowledge-based applications with frame-based and Semantic Web ontologies.
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This program will read in data generated by ABI DNA Analyzers using GeneScan or GeneMapper, CEQ 2000 and SCF instruments and construct gel images which are straightened and sized. Please download and view the tutorial, no documentation is included in 2.1
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