Search Results for "test"
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Showing 38 open source projects for "test"
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Context for your AI agentsBuild data pipelines that feed your AI models and agents without managing infrastructure. Crawl any website, transform content, and push directly to your preferred vector store. Use 10,000+ tools for RAG applications, AI assistants, and real-time knowledge bases. Monitor site changes, trigger workflows on new data, and keep your AIs fed with fresh, structured information. Cloud-native, API-first, and free to start until you need to scale.
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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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...Here present a user-friendly pure Java-based software package, SRICATs, which enable researchers to perform all steps of plant miRNA analysis based on convolutional neural network methods. SRICATs outperforms currently popular software tools on the test data from five plant species: Oryza sativa, Arabidopsis thaliana, Sorghum bicolor, Chlamydomonas reinhardtii and Physcomitrella patens.
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PUMA Repository
Pascal Units for Medical Applications
The PUMA Repository is a collection of Pascal units for medical informatics. It contains reusable source code for a wide field of health-care application development. The code includes a support engine for the European Data Format (EDF and EDF+), converting functions for units of measurement and an HL7 engine. PUMA is compatible with Lazarus and Free Pascal. Some of the units also support other Pascal implementations including Delphi, winsoft Pocket Studio and other compilers. -
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CyberUnits
Class library for computational cybernetics
CyberUnits is a cross-platform class library for rapid development of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal. -
Smart Business Texting that Generates PipelineTextUs is the leading text messaging service provider for businesses that want to engage in real-time conversations with customers, leads, employees and candidates. Text messaging is one of the most engaging ways to communicate with customers, candidates, employees and leads. 1:1, two-way messaging encourages response and engagement. Text messages help teams get 10x the response rate over phone and email. Business text messaging has become a more viable form of communication than traditional mediums. The TextUs user experience is intentionally designed to resemble the familiar SMS inbox, allowing users to easily manage contacts, conversations, and campaigns. Work right from your desktop with the TextUs web app or use the Chrome extension alongside your ATS or CRM. Leverage the mobile app for on-the-go sending and responding.
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MiModD
Mutation Identification in Model Organism Genomes using Desktop PCs
MiModD is a software package for genomic variant identification from next-generation sequencing (NGS) data with optimized usage of system resources and a user-friendly interface. For most model organism genomes it lets the user carry out a complete analysis from unaligned genomic NGS read data to an annotated list of variants on a regular Desktop PC within a few hours. Its user-interface is beginner-friendly and designed to encourage geneticists to analyze NGS data themselves without the... -
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'isotope' is a small command-line utility to calculate the isotope pattern for a given chemical formula. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.
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cdfread is a program for people wirking with mass spectrometry datasets. cdfread implements the routines to read mass spectra and mass chromatograms from data files in netCDF ("Andi-MS") format. Centroid and profile data are supported.
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TVscript
Exploration of the removal of count variable transcripts.
> See TVscript wiki: https://sourceforge.net/p/tvscript/wiki/Home/ Related Software: 1. CStone: https://sourceforge.net/projects/cstone/ 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: (See wiki) 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
... * Article: SYoon, HCTNguyen, YJYoo, JKim, BBaik, SKim, JKim, SKim, DNam, "Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2", Nucleic Acids Research, Vol. 46(10), e60(2018). * PubMed ID: 29562348 * DOI: 10.1093/nar/gky175 -> PLEASE MOVE OR MAKE A COPY OF 'DATA' FOLDER INTO YOUR INTENSIVE TEST FOLDER (I.E. LINUX, MAC OR WINDOWS SPECIFIED FOLDER) TO ALLOW THE PROGRAM TO FIND THE PREDESIGNED DATA. * UPDATE NOTE: -> Sep-1-2020: add an update for Ubuntu-20.04. You will need Boost library installed (sudo apt-get install libboost-all-dev) -> Mar-7-2018: revise header terms in the output file -
Desktop and Mobile Device Management SoftwareDesktop Central is a unified endpoint management (UEM) solution that helps in managing servers, laptops, desktops, smartphones, and tablets from a central location.
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MANTIS R Package
Multi-locus ANTIgenic Simulator R-package for multi-strain pathogens
...For theoretical background please refer to 'MANTIS: an R package that simulates multilocus models of pathogen evolution' (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0598-9 OPEN ACCESS) At the moment, MANTIS is not available on CRAN. To build a source package of MANTIS, use the script buildPackage.R To install MANTIS use 'install.packages(file.tar.gz,type="src",repo=NULL)' To test use test_V3.3_code.R Contact the main author of the publication above for further details. Have fun! -
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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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GenCodeGenerator
C++ class to generate biologically plausible genetic codes
The "GeneticCode" C++ class is designed to generate versions of the genetic code subject to the requirements of the three major models of the genetic code origin and evolution (about these models see, e.g., Koonin & Novozhilov, 2009, IUBMB Life). This class was written specifically to perform statistical test for the paper Makukov & shCherbak (2017), but it might be used for a wider class of studies related to the genetic code. By default, the class "GeneticCode" generates alternative genetic codes, with the reqirement of block structure, and, optionally, with the assumption of stereochemical or biosynthetic models (to impose the assumption of the adaptive model, simply filter the codes using the error_cost() function). ... -
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INTEGRATE: Calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data. To download source code, reference manual and test case, please go to 'Files'. Also refer to 'Wiki' for details.
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PB-sQF_BacterialTyping
Bacterial Typing from either assembled or raw short reads file
Probability Binning - signature Quadratic Form, PB-sQF, types unknown sequence to one of the 628 bacterial library genomes which gives the smallest test statistics thus most similar library strain. The input file is the k-mer counts of the unknown assembled genome sequence or raw short reads file in decimal format generated by KAnalyze developed by P. Audano et al. (https://sourceforge.net/projects/kanalyze/). The download included the library index, the library name and sample unknowns. -
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ChelomEx
Isotope assisted discovery of metal chelating agents from LC-MS data
ChelomEx identifies chromatographic features of metal complexes and associated free ligands or other related adducts in high-resolution LC-MS data. A built-in graphical user interface and compound library aid in the efficient evaluation of the results. If you use ChelomEx for your research, please cite our Analytical Chemistry paper that describes the software (http://dx.doi.org/10.1021/ac503000e). To comment, send bug reports or suggestions for additional features to be implemented... -
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fast_count_multi
Extremely fast NGS read counter
Counts NGS read alignments against GTF annotations in a multithreaded and scalable fashion. Benchmark: 8 core 1M annotations for 2Gb sorted reads ~30 seconds compared to ~28 minutes for bedtools multicov. Files include: fast_count_multi - reports all counts and RPKM, multithreading support fast_count_deseq - reports gene counts in deseq compatible format, multithreading support fast_count - reports all counts with no multithreading support. usage ./fast_count_multi... -
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The Protein Similarity Network
Human protein similarity network used to predict drug safety.
...We found that this network is particularly useful to distinguish approved from problematic drug-targets. Here you also find the complete set of programs and datasets we used for this purpose. Free to help further test and develop this project. Your help and expertise are much appreciated ! If you have any questions, please do not hesitate to contact us in the forum or by email. Please see the original manuscript: Lopes, TJS, et al. (2015) - "Identifying problematic drugs based on the characteristics of their targets" - Frontiers in Pharmacology doi: 10.3389/fphar.2015.00186 -
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Toolchain for quantification of fluorescence intensity and morphological parameters in single cells using microscope based cytometry.
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FASTQSim
NGS data characterization and in silico read generation
...To create training or testing datasets, FASTQSim has the ability to convert target sequences into in silico reads with matching error profiles. 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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GUItars
GUItars is designed for the analysis of high throughput RNAi data.
...The program can handle the analysis for screens without replicates as well as with replicates. For comparison purposes, non-SSMD-based methods such as percent activity, z-score, and t-test are also provided as scoring options. Version 2.1 released: several bugs fixed. Version 3.0 released for Windows and Mac: experiment-wise analysis option, map to all samples option (no hit cut-off needed), percent activity for replicates option and .ai output format are added -
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qPMerge
phospho-peptide merge tools for Galaxy
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msBayes allows complex and flexible phylogeographic inference. More specifically, you can test the simultaneous divergence (TSD) of multiple population (species) pairs. It uses approximate Bayesian computation (ABC) under a hierarchical model.
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compare-results
Program comparing Simulation Results for the SBML TestSuite
Compare SBML Test Suite Results =============================== The [SBML Testsuite](http://sbml.org/Facilities/Online_SBML_Test_Suite) allows developers of ODE based simulators to test their implementation against a large number of test cases that test a wide aspect of the [SBML Specifications](http://sbml.org/Documents/Specifications). While implementing my simulator [RoadRunner](http://roadrunner.sf.net) I wanted to be able to compare it using a wider range of parameters: - filter for new tests - filter for tests with specific tags - mark elements that I know I did not implement -
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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.
