Search Results for "statistical"

The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.

...VFS combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. Source code with user manual and installation guide of VFS is available at sourceforge's "Files" section. Citation: http://www.ncbi.nlm.nih.gov/pubmed/

...We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data. Comparing with the existing software PVAAS, our method has several advantages such as stringent rule-depended filters and statistical filters in each step, detection sequence variants for known splicing events, identification sequence variants in two parts of splicing (junction) separately, detection junction shift events if providing known splicing annotation, evaluating splicing signal, comparing with known DNA mutation and/or RNA editing data, and short running time.

Corbata is a set of statistical tools that can be used to analyze the core microbiome across a set of samples.

...It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in multiple samples simultaneously and identify differential proportion of RNA editing events in different samples. Moreover, the genome variation can be easily removed by a subprogram fish.pl in our package.

...Please visit the new IRSTLM official website: http://hlt-mt.fbk.eu/technologies/irstlm IRSTLM: A tool for the estimation, representation, and computation of statistical language models. IRSTLM, the IRST Language Modeling Toolkit, features algorithms and data structures suitable to estimate, store, and access very large n-gram language models. Our software has been integrated into a popular open source Statistical Machine Translation decoder called Moses, and is compatible with language models created with other tools, such as the SRILM Tooolkit.

Report historical and statistical running time of system and other components, keeping it between reboots. Like uptime command but with more interesting output. NOTE: Tuptime was completely rewriten in python and now its available in https://github.com/rfrail3/tuptime

The Thot toolkit repository has moved to http://daormar.github.io/thot/ Thot is a toolkit for statistical machine translation. The new Thot toolkit includes fully automatic and interactive machine translation, incremental training of statistical models, parallel estimation, ...

Processing of smallRNA-Seq data to gather biologically relevant information requires application of multiple statistical and bioinformatics tools from different sources, each focusing on a specific step of the analysis pipeline. The analytical workflow can be challenging for the continuous interventions by the operator, a critical factor when large numbers of datasets need to be analyzed at once. To allow a flexible and comprehensive analysis of smallRNA-Seq data we designed a novel modular pipeline, called iMir, integrating multiple open source modules and resource in an automated workflow, devising different statistical approaches to analyze data rigorously. iMir comprises also a Graphical User Interface (GUI), so that the pipeline is particularly suited for biologist and early stage bioinformaticians and produces both graphics and text outputs.

MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in...

QUASI is a toolkit to rapidly assess the quality of shRNA-Seq based data and call differential abundance using common statistical inference methods (DESeq, edgeR, baySeq).

...Open XDMoD has been developed to provide detailed information on resource utilization and performance for academic and industrial HPC centers. More information is available at http://xdmod.sourceforge.net/ UBMoD is a data warehouse and web portal for mining statistical data from resource managers in high-performance computing environments. UBMoD presents resource utilization over set time periods and provides detailed interactive charts, graphs, and tables.

YaaCs, developed by Demetra www.opinioni.net, survey research via phone CATI (also Voip) and web CAWI and for telemarketing. Develop questionnaire for survey, create probabilistic sample, monitoring Interviewer, export survey data in statistical.. It's integrate with www.modsurvey.org. Sviluppato da Demetra www.opinioni.net per indagini CATI/ CAWI e CAMI. Vi permette di programmare dei questionari elettronici, campionamenti, monitorare gli intervistatori, esportare dati in formati statistici. E' integrato con www.modsurvey.org.

GAAS (Genome relative Abundance and Average Size) is a bioinformatic tool to calculate accurate community composition and average genome size in metagenomes by using BLAST, advanced parsing of hits and correction of genome length bias.

The Moses repository has moved: https://github.com/moses-smt/mosesdecoder Factored phrase-based, hierarchical and syntax decoder for statistical machine translation

ANDES. This is a library and a set of applications that can be used to analyze the results of deep sequencing results. (See Li et al.: ANDES: Statistical tools for the ANalyses of DEep Sequencing. BMC Research Notes 2010 3:199.)

CODD is a tool for creating and analyzing statistical measures of "developer involvement" in free software projects.

STATPerl (Statistics with Perl) is a free Statistical Software based on Perl. Perl source codes for various statistical analysis are given with it. User can add new analysis and edit existing one. An inbuilt Perl IDE comes with it.

REAR or (Realtime Equity Analysis and Reporting) is a tool which employs a Perl front-end engine for capturing real time equity data, then analyzing the raw data using the CPAN-R statistical analysis Engine and generates a detailed user report

Everyday Software for the Researcher of Restricted Means: This project is intended to offer scientists and students with small budgets advanced versions of aqua-built desktop-editing, graphics and statistical applications for MacOSX.

This small, sharp tool generates SVG charts and graphs for use in other processes. This could easily be used to generate dynamic charts for web sites, statistical displays or other data visualization in a fully-scalable way.

A statistical view of the recorded activity on a Honeynet. A mechanism for a honeynet to present some information about its findings over the web. This is done by a statistical analysis on the inbound firewall logs recorded by the honeynet's firewall.

Parses log information for the courier mail systems and presents statistical summary information in a variety of formats.

Scripts and hub mods written to enhance OpenDCHub. The Hub-Security script filters unregistered users by country, and adds op commands and security features. Statistical and fun scripts are also available. Future development will shift towards ODCH mods

SpamWizard is a statistical spamfilter working at serverlevel. It's based on Paul Grahams essay "A Plan for Spam", and has evolved to include several other features and filtering techniques. Supports *nix platform.