Search Results for "dna sequence analysis"
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Showing 28 open source projects for "dna sequence analysis"
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Creatio Low-Code Development PlatformIntelligent low-code platform to empower both IT and non-IT staff to effortlessly build enterprise-grade apps and processes
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Create engaging surveys on your tablet or computer with ease.Create great-looking surveys, forms, polls, voting, questionnaires, NPS, customer satisfaction, customer experience, employee satisfaction surveys... on your computer or tablet, customize the look of your survey however you like, & display collected data with eye-catching and insightful graphics.
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XLibraryDisplay
A sequence analysis tool for protein engineering
XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
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ReachabilityAnalysis.jl
Compute reachable states of dynamical systems
Reachability analysis is concerned with computing rigorous approximations of the set of states reachable by a dynamical system. In the scope of this package are systems modeled by continuous or hybrid dynamical systems, where the dynamics change with discrete events. Systems are modeled by ordinary differential equations (ODEs) or semi-discrete partial differential equations (PDEs), with uncertain initial states, uncertain parameters or non-deterministic inputs. -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data. -
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OmicsSuite
OmicsSuite: a suite for multi-omics analysis and visualization.
OmicsSuite (https://github.com/OmicsSuite/, https://omicssuite.github.io), original name BioSciTools, a desktop program developed based on Java 11, aims to make new exploration and contribution to the development of bioinformatics, and realize data analysis and visualization in the fields of sequence analysis, multimomics (transcriptomics, genomics, protein omics, metabonomics, single cell), microbiology, clinical, etc. The program inherits the excellent interactive components, perfect analysis function and beautiful operation interface of HiPlot (https://hiplot.cn), which I developed based VUE.js and Node.js, etc. -
Dragonfly | An In-Memory Data Store without LimitsDragonfly is a drop-in Redis replacement that is designed for heavy data workloads running on modern cloud hardware. Migrate in less than a day and experience up to 25X the performance on half the infrastructure.
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dnaasm
set of tools for NGS data analysis
genome de novo assembler for next generation sequencing data, tool to link contigs by long DNA reads -
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LUAD
Code used for the data analysis
Identification and validation of novel DNA methylation markers for early diagnosis of lung adenocarcinoma -
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MarDRe
MapReduce-based tool to remove duplicate DNA reads
MarDRe is a de novo MapReduce-based parallel tool to remove duplicate and near-duplicate DNA reads through the clustering of single-end and paired-end sequences from FASTQ/FASTA datasets. This tool allows bioinformatics to avoid the analysis of not necessary reads, reducing the time of subsequent procedures with the dataset. MarDRe is the Big Data counterpart of ParDRe (link above), which employs HPC technologies (i.e., hybrid MPI/multithreading) to reduce runtime on multicore systems. ... -
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GMOL
A tool for 3D genome structure visualization
GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group. 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. The project... -
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ImagingAnalysis
Direct tissue-level image quantification package for Mathematica
ImagingAnalysis is a Mathematica package that performs grid-based analysis of time-lapse imaging data saved in a sequence of TIFF files. This package requires Mathematica 7.0. Revised on 14 May 2017: Bugs are fixed and incompatibility issues are resolved. The current version runs on Mathematica 11. -
Multi-Entity Cloud Accounting Software for Growing BusinessesBuilt natively on the Microsoft Power Platform (Dynamics 365), Gravity delivers robust multi-entity financial management with seamless integration to Microsoft 365, Power BI, Teams + Copilot — no third-party add-ons required.
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CANStream
An applicaton for CAN bus coms development, testing and validation
CANStream is a .NET application intended to be used for CAN (Controller Area Network) bus communication development, testing and validation. CANStream allows to extensively test any system using CAN communication by sending and receiving CAN frames. Thanks to its powerful built-in mathematical expression evaluator, CANStream can also behave as a real control system feeding back the test device or commanding a third party device with context sensible data. Extended data logging and data... -
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Tool support for creating FMC* diagrams [Block diagrams, Petri nets, Entity-Relationship diagrams (ERD)] in MS-Visio 2000 and newer. Features: stencils, consistency checking, Petri net simulation, exporter e.g. pdf, ... *Fundamental Modeling Concepts A stripped down version of the stencil set is available for TAM (Technical Architecture Modeling of SAP). This set uses UML notation and contains Block, Activity, Sequence, State, Class, and Component diagrams. It doesn't contain Simulation,...
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HBS-tools
a set of tools for hairpin bisulfite-seq data analysis
The emerging genome-wide hairpin bisulfite sequencing technique facilitates the determination of DNA methylation fidelity and accurate methylation calling. Here we present HBS analyzer, the first command line based open-source tool to process genome-wide hairpin bisulfite sequencing data. It accepts Illumina paired-end sequencing reads as input, performs alignment to recover the original (pre-bisulfite-converted) DNA sequences and calls methylation status for cytosines on both DNA strands. -
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MSCViewer
A tool for visualization and analysis of logs as sequence diagrams
MSCViewer is a tool intended for debugging of control flows in concurrent, distributed systems. The tool loads logs generated by various entities in the system and visualize a sequence diagram chart for events and interactions. The diagram is fully interactive: entity can be added/removed from the diagram and shuffled; events can be filtered, searched, highlighted and annotated with comments. MSCViewer features integration with a Python interpreter which allows writing Python scripts... -
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chipexo
model based analysis of ChIP-exo data
Here we developed a novel analysis framework named MACE (model-based analysis of ChIP-exo) dedicated to ChIP-exo data analysis. MACExo has the following four steps: 1) sequencing data normalization and bias correction; 2) signal consolidation and noise reduction; 3) single nucleotide resolution border detection using Chebyshev Inequality; and 4) border matching using Gale-Shapley’s stable matching algorithm. -
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ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW. ...
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COV2HTML
A visualization and analysis tool of Bacterial NGS data for Biologists
COV2HTML provides an easy and 'in home' web interface for biologists that allows coverage visualization of the NGS alignment needed for the analysis. It combines two essential processes: (i) MAP2COV, a tool that converts the huge NGS mapping or coverage files into light specific coverage files which contains genetic elements informations. (ii) COV2HTML, a visualization interface allowing a real-time analysis of data with selected criteria. Thus this interface offers a visualization of NGS mapping coverage data (DNA-seq, RNA-seq, ChIP-seq and TSS) performed in different prokaryotic organisms (bacteria, viruses...) or different experimental conditions (mutant versus wild type strains or different growth states…) facilitating studies. -
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DNAA is the DNA analysis package, for analyzing next-generation post-alignment whole genome resequencing data. Specifically, DNAA is able to find structural variation, SNP and indel variants, as well as evaluating the mapping and data quality.
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Linear Program Solver
Solve linear programming problems
...The main features of LiPS are: ● LiPS is based on the efficient implementation of the modified simplex method that solves large scale problems. ● LiPS provides not just an answer, but a detailed solution process as a sequence of simplex tables, so you can use it for studying/teaching linear programming. ● LiPS gives sensitivity analysis procedures, which allow us to study the behaviour of the model when you change its parameters, including: analysis of changes in the right sides of constraints, analysis of changes in the coefficients of the objective function, analysis of changes in the column/row of the technology matrix. ... -
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NGS data quality evaluation
Python tool to evaluate the quality of high-throughput sequencing data
...The evaluation is performed in a genomic region defined by the user, and it provides some statistics computed from the reads that map to that region (ie. a single gene). The program provides a graphical output embedded in an html file. The analysis contains the sequencing quality along the reads, the mapping quality distribution, the coverage of the defined region, the overall quality at each nucleotide position, and the distribution of the coverage as a function of the GC content in the reference genome. The results provided by this program can help to distinguish between sequence variation and sequencing errors. -
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The project would include the development of XUL, CSS and Javascript components to assist biologists in sequence manipulations, data mining, data analysis, etc.).
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Skittle Genome Visualizer
Skittle Development MOVED to Github
Skittle is a 2D visualization of genome sequence files. The program assigns four colors to the four nucleotides and text wraps the sequence to create a 2D picture based on the DNA sequence. Great for researching tandem repeats and chromosome structure. Compiled downloads available at http://dnaskittle.com/ Source maintained at https://github.com/josiahseaman/skittle -
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Swift is an open source package for primary data analysis on next-gen sequence data "from images to basecalls". Currently Swift is targeted toward Solexa/Illumina sequencing, but is designed to be platform agnostic.
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JRET (Java Reverse-Engineering Tool) is a program that is capable of reconstructing sequence diagrams from JUnit testsuites through dynamic analysis. It is written in Java/AspectJ and provides a GUI as well as command-line possibilities.
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HyPhy is a comprehensive environment for maximum likelihood statistical analysis of genetic sequence data. It includes a large collection of out of the box analyses, a feature-rich graphical user interface for custom data analysis and a scripting languag
