Search Results for "coverage" - Page 10
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Showing 421 open source projects for "coverage"
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oovcde
C++ analysis IDE with auto class, sequence, zone, dependency, diagrams
The Oovcde project has been renamed to OovAide. Downloades from either location work for now. The Oovcde project is a C++ IDE for Windows or Linux with an automated multi-tasking build system, cross compiler support, an analysis tool based on CLang that creates UML class, component, sequence as well as zone and portion diagrams from C++ source, static analysis and test coverage. The diagrams allow navigation through the source code, and can be edited manually and saved as .SVG files... -
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VarScan
Variant detection in next-generation sequencing data
Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes. THE LATEST VERSION IS AVAILABLE ON GITHUB -
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Trowel - Sequencing Error Corrector
Error Correction Module for Illumina Sequencing Reads
Trowel is an error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach. This tool is the first tool that uses a quality threshold instead of a coverage cutoff in order to extract trusted k-mers. This tool guarantees high accuracy and speed. This tool has been developed since 21. Jan. 2013 by Euncheon Lim in Prof. Dr. Detlef Weigel's Lab in Max-Planck Institute for Developmental Biology. First of all, you have to install the exact version of boost... -
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Fontaine is a new font analysis program. The program produces reports that document font features and Unicode coverage. Report output is available in various human readable TEXT, XML, and JSON formats.
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That project aims at providing a clean API and a simple implementation, as a C++ library, of a Travel-oriented Distribution System. It corresponds to the simulated version of the real-world Computerized Reservation Systems (CRS).
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That project aims at providing a clean API and a simple implementation, as a C++ library, of an Airline-related Inventory Management system. That library uses the Standard Airline IT C++ object model (http://sf.net/projects/stdair).
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SPAT
Satellite Power Analysis Tool
# Satellite Power Analysis Tool (SPAT) The tool was originally created to aid during the Satellite Power System design process, however it has evolved to a Satellite Missoin design tool. The user defines the mission and the Satellite design paramenters and, the tool will output: - Power analysis - Battery charge/discharge analysis - Link budget - Ground track coverage - Ground station visibility SPAT has been developed in MATLAB and MCR (Matlab runtime) is required. SPAT... -
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Templatious
Generic C++11 template library
Generic C++11 template library to eliminate often occurring boilerplates in everyday situations. -
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fitGCP
Fitting genome coverage distributions with mixture models
Genome coverage, the number of sequencing reads mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference genomes often remain unaccounted for. Making... -
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Cobertura is a free Java tool that calculates the percentage of code accessed by tests. It can be used to identify which parts of your Java program are lacking test coverage. It is based on jcoverage.
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Digital Expression on the Web
DEW is a platform that allows users to explore RNA-Seq data
... estimates effective expression profiles and a corrected alignment is produced. For each gene the user provides, DEW computes coverage descriptive statistics (RPKM, FKMP and total, mean and median corrected counts), expression profiles (normalized as R/FPKM and trimmed mean of fold change). DEW allows users to explore the data by providing interactive graphs. -
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MERAP
Medical Resequencing Analysis Pipeline
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TracerJD
Trace-based Dynamic dependence analysis via Fine-grained Logging
TracerJD project website: www.nd.edu/~hcai/tracer TracerJD video demo: http://youtu.be/HR_rNX9K5IU TracerJD is a program execution Tracer for Java dynamic Dependence analysis. The major goal of this framework is to enable fine-grained dynamic dependence analysis for Java program based on program execution traces. It is developed in support of a wide range of dynamic dependence-based analyses such as those used in software testing, debugging, and evolution tasks. With TracerJD, we... -
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unit test quality analyser
JUnit Test Quality Analyser
Unit test quality is not determined only by coverage but by javadoc and asserts as well. This plugin will act as a guide to developers when writing unit tests. Managers/Leads can also verify the quality of unit tests delivered by developers through it, and hence ensuring that budget is being well spent -
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mirUtils
miRNA alignment quantitation based on miRBase annotations
mirUtils provides quantitation of aligned microRNA sequences based on miRBase annotations. Starting from a miRBase-aligned BAM/SAM file, mirUtils reports counts and quality metrics for several taxonomy levels, including miRNA precursor hairpins, hairpin groups and families, mature miRNA loci, mature sequences, and genomic clusters, as well as per-hairpin-position alignment start and base coverage details. -
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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... -
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NGSimple
NGS - Next-Generation Sequencing sIMulation PipeLinE
This pipeline, mainly written in perl is designed to simulate NGS parameters (illumina sequencing type, read length, insert size and coverage) based on a given reference, and give a report to choose the best parameter combination that could contribute to a good assembly. simulation.pl generates simulated reads from a reference in fasta format. It's recommended to start with a short reference (~5M bases), in case that the number of generated reads is too large for assembly... -
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SMPP-Binder
Integrate your application though a simple SMPP Linux shell command
This Little script allows you to communicate with any SMSC and send a SMS in a easy way. If your application needs to send a single, simple SMS you will only need to invoke this script with the right parameters. Also is useful in order to check routing coverage. -
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testgeneration
Generation of test suites from test specifications
Test suites developed for complex software systems contain thousands of test cases. Keeping track on the test coverage and changing the test suite as the system requirements evolve can consume significant efforts. Testers have to implement or generate test scripts containing thousands of isolated executable test cases. Each single test case should be so simple enough so that test results can be easily evaluated. Often it makes code duplication in the test code unavoidable. If every test script... -
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SerialToFS
Program handling file operations when interfacing embedded system.
Program handling file operations when interfacing embedded system by serial port. Main intention for creation of this program was getting files with code coverage out of the embedded system memory. -
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BRACIL
ChIP-seq analysis tool
Binding Resolution Amplifier and Cooperative Interaction Locator (BRACIL) is a blind-deconvolution model that integrates ChIP-seq coverage with motif discovery. BRACIL predicts binding site locations with high-resolution and also cooperative interactions in ChIP-seq data. -
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Arabic Unknown Words
Arabic Unknown Words, or words not included in Buckwalter Morphology
... fit to include in a dictionary. Proper names are not filtered out because high frequency proper names are usually included in morphological analysers to improve coverage, but in dictionaries people might want to exclude them. -
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X10 code coverage tool
A prototype code coverage tool for x10
A code coverage tool for x10 using Jacoco -
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CoDeCZ
Derive copy number status from targeted sequencing data
CoDeCZ derives copy number state from targeted sequencing data on gene or exon level. Results are NOT true copy number however, but they are semi-quantitative: It uses the modified z-score to calculate deviation in normalized coverage per specified region. The higher the Z-score, the higher the copy number. The final z-score depends on the quality of the data and the makeup of the reference pool.