Search Results for "/storage/emulated/0/android/data/net.sourceforge.uiq3.fx603p/files" - Page 16
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Showing 1243 open source projects for "/storage/emulated/0/android/data/net.sourceforge.uiq3.fx603p/files"
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Insulin IP Calc
Insulin infusion protocol calculator
A simple, point of care, clinic decision support system (CDSS) Android app for Insulin infusion and hyperglycemia management in the ICU. The infusion protocol calculator is based on the updated "Yale Insulin Infusion Protocol" http://bit.ly/1DaVfUd and American Association of Clinical Endocrinologists (AACE) blood sugar targets. http://inpatient.aace.com/ . Source code requires Xamarin Studio & Android SDK to compile. -
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oasis-genomics
Oasis Genomics cancer omics integration portal
OASIS is an application that enables complex analytical queries across somatic mutations; copy number changes (CNV); and gene expression data. OASIS has been built on top of the BIoMart frameworks and has been extended to incorporate unique tools and visualizations to facilitate analysis of complex cancer "Omics" datasets. -
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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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Toolkit for processing genetic data. Currently supports (command-line): Half-IBD (Identity by descent) aka HIRs - between 2 or any number of files (in distances and cM); RAW2PED, PED2RAW conversions; regions of homozygousity and other converters.
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FMFilter
Fast Model Based Variant Filtering Tool
...It has the capability to filter with control individuals and eliminate the majority of the false alarms specific to a population. It requires negligible memory which enables to handle very large variant files in ordinary computers. -
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bsclient
An interactive FTP-like command-line BaseSpace download client
bsclient is an interactive text-based client for browsing and downloading files from Illumina BaseSpace. It has a simple interface simliar to FTP and can be used to easily download files onto a remote server or in any situation when the web-based interface is not accessible or desirable. Please note that current development on this project has moved to GitHub: https://github.com/jvolkening/bsclient -
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...Prokaryotic Proteogenomic Tool(PPT) is developed as a part of GenoSuite framework. PPT is for finding novel translations in prokaryotic genomes and is dependent on Mass Spectrometry based proteomics data and related genome sequence. Some Key features of the tool are.... (1) Configured for 4 open source algorithms to perform database searching for peptide identification. Any combination of the 4 algorithm can be chosen. (2) Lists out the genome search specific peptides(Novel peptides). (3) Spectral matches can be visualized for the quality assessment...
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SoftSV
Calling structural variations. The soft way.
SoftSV is a tool for the detection of small and large deletions, inversions, tandem duplications and translocations from paired-end sequencing data. It uses aberrant paired-end mappings to determine approximative breakpoint regions and refines the breakpoints by analysing soft-clipped sequences for potential split-reads. For more information about the algorithm and an evaluation, have a look at this publication: "Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms" (PMID 25998133) Please cite this artilce if you used SoftSV in your publication. -
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A set of tools for working with VCF files, such as those generated by the 1000 Genomes Project. This project is migrating to github: https://vcftools.github.io/
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10
swathTUNER
Software tool for optimizing data-independent acquisition methods
SwathTUNER combines usability and flexibility for the selection of different SWATH data acquisition strategies to address the requirements of multiple experimental conditions. It can be used for any acquisition instrument, including FT-based analyzers, where the same principles with respect to variable precursor isolation windows apply. Fixed and variable windows based on equalizing the distribution of either the precursor ions or the total ion current within each window can be created. -
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TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological "parts". Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.
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SPA
SPA: a short peptide assembler for metagenomic data
...A nucleotide assembly-based strategy does not fare much better since metagenomic assemblies are typically very fragmented and also leave a large fraction of reads unassembled. We present a method for reconstructing complete protein sequences directly from NGS metagenomic data. Our framework is based on a novel Short Peptide Assembler (SPA) that assembles protein sequences from their constituent peptide fragments identified on short reads. We also present a new implementation of SPA based on suffix array (SFA-SPA) which runs significantly faster than SPA. Youngik Yang, Cuncong Zhong, and Shibu Yooseph* J. ... -
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LDhat
Estimate Recombination Rates from Population Genetic Data
LDhat is a package written in the C language for the analysis of recombination rates from population genetic data. This package has migrated to github: https://github.com/auton1/LDhat -
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MDA
Molecular Dynamics Analyzer (MDA)
...The particle fitting routine is provided by an external library written in C. The results can be exported into the Matlab Workspace or the trackID, frameID and xyz coordinates are saved into files. -
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mAPV
modified Asymmetric Pseudo-Voigt Model
A new peak detection algorithm for MALDI mass spectrometry data based on a modified Asymmetric Pseudo-Voigt model -
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Library of various Java Swing user interface components, with emphasis on views and editors for complex data structures, like collections, sets, lists, maps, graphs, and matrices.
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This is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). It supports symbolic math, optimization, continuation, data analysis, biological apps...
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TRiDaS is a universal data exchange standard for the dendrochronology community. This project contains the data standard itself as well as libraries and tools useful for reading, writing and converting dendro data files.
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ConvertMAS
ConvertMAS converts Chemical File Formats mol, mol2 and sdf.
ConvertMAS - molecule converter; use to convert Chemical File Formats. It works on mol, mol2 and sdf files. It converts single file to respective formats. It will split sdf file with multiple molecules into seperate single files of any desired format. Also ConvertMAS creates sdf files from joining of mol, mol2 and sdf files. This is stand alone application; hence no need of internet connectivity to get results. It will generate output files in less time. ... -
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ESBTL (Easy Structural Biology Template Library) is a lightweight C++ library that allows the handling of PDB data and provides a data structure suitable for geometric analysis and advanced constructions.
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ReseqTrack is now hosted at github: https://github.com/EMBL-EBI-GCA/reseqtrack ReseqTrack is a mysql database and perl api for tracking files associated with resequencing projects and running analysis pipelines on resequencing data.
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BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.
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PRIMUS
Pedigree Reconstruction and Identification of a Maximum Unrelated Set
NEW: Download new version with Pedigree Reconstruction at primus.gs.washington.edu This versions is outdated and incomplete. Please visit the new website for the complete version of PRIMUS. We present a method adapted from graph theory that always identifies the maximum set of unrelated individuals in any dataset, and allows weighting parameters to be utilized in unrelated sample selection. PRIMUS reads in user-generated IBD estimates and outputs the maximum possible set of unrelated... -
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cusAPV
customized Asymmetric Pseudo-Voigt Model
A new peak detection algorithm for MALDI mass spectrometry data based on a customized Asymmetric Pseudo-Voigt model -
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...Also, merlin includes tools for the compartmentation of the model that predict the localisation of the proteins encoded in the genome, and thus the localisation of the metabolites involved in the reactions induced by such proteins. Finally, merlin expedites the transition from genome-scale data to SBML metabolic models, allowing the user to have a preliminary view of the biochemical network.
