Search Results for "tool test"
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Showing 16 open source projects for "tool test"
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QUAST
Quality Assessment Tool for Genome Assemblies
QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. It is maintained by the Gurevich lab at HIPS (https://helmholtz-hips.de/en/hmsb). For the most up-to-date description, please visit http://quast.sf.net. Below are just some highlights. QUAST computes several well-known metrics, including contig accuracy, the number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper and manual). A... -
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ReViMS
ReViMS, a 3D volume rendering tool for light-sheet/confocal microscopy
Reconstruction and Visualization from Multiple Sections (ReViMS), an open-source, user-friendly software for automatically estimating volume and several other features of 3D multicellular aggregates (i.e., cancer spheroid, zebrafish, fruit fly). ReViMS requires a z-stack of 2D binary masks, obtained by segmenting a sequence of fluorescent images acquired by scanning the aggregate along the z axis, using a confocal or a light-sheet fluorescent microscope. It provides a number of tools... -
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ntx
Neutrality tests using the SNP site frequency spectrum
Tests on "neutrality" are designed to detect systematic deviations from chance patterns in genetic data. This tool computes for a given SNP site frequency spectrum some standard test statistics like Tajima's D, Fay & Wu's H, etc. Additionally, the user may adapt the tests to specific demographies by specifying non-standard first and secondary moments. These can be obtained e.g. from simulations. -
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CusVarDB
CusVarDB generated variant protein database from NGS-datasets
...Download the annotation (ANNOVAR) database and Dry-run concept to customize the commands Executables are available at http://bioinfo-tools.com/Downloads/CusVarDB/V1.0.0/ Test dataset is available at http://bioinfo-tools.com/Downloads/CusVarDB/V1.0.0/test_dataset.rar -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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MethyMer
Design of specific primer combinations for bisulfite sequencing
MethyMer is a Python-based tool aimed at selecting specific primers for amplification of complete CpG islands. These regions are difficult in terms of selection appropriate primers because of their low-complexity, polyN-, CG-richness, etc. MethyMer have a flexible scoring system capable of selecting primers in problematic regions (e.g. SpG islands) and includes specificity test (based on bowtie alignment against bisulfite-treated genome). -
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CvMob is an Open Source tool to automatic visual analysis of human movement. The software calculates the optical flow to generate data about trajectory, velocity and acceleration using low-quality videos. For more informations, please visit our website: http://www.cvmob.ufba.br/
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CorNetMap
A tool for Gene Expression Correlation Network
Capabilities of CorNetMap: 1. Read data as tab-delimited text file. Can be used for analysis of any data set beyond gene expression. 2. Capable of both two-dimensional and multidimensional data analysis. 3. Calculate Pearson correlation and cross-correlation for analysis data with phase difference. 4. Generate correlation Heat-map and draws network map. 5. Save correlation data as text file. How to use and doccumentation:... -
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ISVASE
identification of sequence variant associated with splicing event
To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently by RNA splicing mechanism. It is to be noted that about one third or a half of all disease-causing mutations effect RNA splicing. However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data.... -
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FASTQSim
NGS data characterization and in silico read generation
...FASTQsim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software. In this regard, in silico datasets generated with the FASTQsim tool hold several advantages over natural datasets: they are sequencing platform independent, extremely well characterized, and less expensive to generate. -
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Used to record and analyze some behavioural experiments in neuroscience (using usb webcam). it was developed in collaboration with neuropharmacology lab at Faculty of Medicine, Ain Shams University. it can use(JMF,OpenCV,JMyron & AGCamLib) for webcam
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FishingCNV
Copy number variation (CNV) detection in exome sequencing data
FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases. -
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ClinStudyWeb is designed to provide a flexible infrastructure for managing patient and assay data from clinical studies. It uses a plugin system for study-specific web forms and arbitrarily complex test classifiers, and supports XML import/export.
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RNAseqR
RNA-seq expression analysis tool
RNAseqR is designed for expression analysis of RNA-seq data, and is best suited for analysis of multiple, unreplicated libraries. It is a C++ coded program currently compiled for Linux systems. With GUI and command line interfaces, it can do log, PPM, and/or RPKM (if lengths provided) transformations, as well as, statistical analysis for differential expression, using the negative binomial cumulative distribution function (CDF) or the R test statistic introduced for EST analysis by... -
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clinicalStudyTracker
Clinical study tracker tracks case study members through activities.
Developed at Medical Research Council UK to meet a common clinical trial need to track various types of clinical data. Users log dates of completed tasks against participant ID. Simple, useable, reduces lost data! Makes graphical progress reports. -
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BCAR is a library for the associative classification, which denotes "Boosting Class Association Rules". BCAR provides a general tool for classification tasks with various types of input data.
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Our software can test for HLA allele and amino-acid differences between two populations. It examines zygosity, tests for strongest association, interaction & linkage disequilibrium among amino acid epitopes.
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