Open Source Data Analytics Tools - Page 9

During the past few years, whole exome sequencing has imposed itself for genetic research, largely due to its use for detection of causative mutations responsible for Mendelian disorders. As a consequence of their power and of the rapidly decreasing cost of these technologies, massive amount of exome sequencing data are generated and becoming available to a broadening community of scientists. However, these data remain difficult to analyze and interpret by the general scientific community, due to the limited bioinformatics resources that are currently freely available for their analysis and the partial information that they provide. Here, we present an interactive and free analysis package, ExAM, dedicated to whole exome sequencing data analysis. It is accessible to non-computer scientists and provides a complete set of information, as well as decision support to prioritize candidate disease causing variants.

Open, extensible web-based collaborative platform for microarray gene expression, sequence and PPI data analysis, exposing distinct chainable components for clustering, pattern discovery, statistics (thru R), machine-learning algorithms and visualization

EyeMap is a visualization and analysis tool for text reading eye movement data. It can process Unicode, proportion/non-proportion and spaced/unspaced reading materials, which supports various languages and experiment methods.

Feather is a fast, interoperable binary data frame storage format designed for efficient data exchange between analysis tools. It provides columnar serialization for data frames, making read and write operations faster than many text-based formats. The project was built to make sharing data across languages such as Python and R easier. Feather is powered by the Apache Arrow columnar memory specification, which helps it represent numeric, string, categorical, date, timestamp, boolean, and binary data efficiently. It also supports null and missing values across column types. Current development continues through Apache Arrow, with modern Python usage handled through pyarrow.feather.

The project has been created to develop a software that can help scientists in the area of physical chemistry with focus on foods data analysis tools that are currently mainly done by hand. In the first step, advanced analysis of texture analyzer compression data are provided and the project will be extended over time dependent on the time I can get to continue with it.

A simple Windows application for data of atomic force spectroscopy (force-distance curves) analysis. It is adopted for Veeco/Bruker Picoforce file format, but it is possible to use it for analysis of txt-table data.

FreeFlow is web-based system, written in php, designed to facilitate high-throughput analysis of flow cytometry data for drug discovery. It processes and maintains flow cytometry data and is coupled with data analysis and visualization tools.

FreeQDA is a software for professional qualitative research data analysis, such as interviews, manuscripts, journal articles, memos and field notes.

FwPlatinum provides real time data analysis of CheckPoint FireWall-1 connection logs. Data is stored for up to 2 years, and is accessed by CGI generated graphs which can drill down to the specific time that you are interested in.

GAPE is a one-stop proteogenomic informatics software that provides a multifaceted and standard workflow against eukaryotes in proteogenomic data-analysis cycle for genome refinement and global identification of PTM events. This software allows concurrent querying of proteomic and genomic databases to refining the genome and proteome annotations comprehensively. This includes MS data and database construction, database searches, FDR calculations, statistical result integration, validation of annotated genes, identification of previously unidentified genes, protein level identification of alternative spliced variants and SAAV, biological interpretation, and global PTM discovery.

GCDPlot is a Microsoft Excel VBA program for geochemistry and geology data analysis. GCDPlot can use the Microsoft Excel data to plot scatter, ternary chart and discrimination diagrams that can be add, delete and modify by user.

This is the beta-version of a shape-based peak calling tool for ChIP-Seq data analysis. It is built using Generalized Linear Model with Negative binomial distribution. This tool accounts for the common peak shape, local variability of peak shifting distance and negative binomial background noise.

GNUexp is a GNUstep/Cocoa framework and a collection of tools helping you to plan, develop, and administer applications associated with visual psychophysics, experimental psychology and statistical data analysis.

GODASM is the brief of ".Gff Organized Data Analysis System for Microarray Studies". Private programs, GODA system, had been successful developed in 2008 at CGMH,Taiwan. Now the project will transfer GODAs to open-source based system.

GRAIL Real Time Location Service (RTLS)

GSCope3 performs microarray data analysis to find correlations between BLSOM clusters and any form of omic knowledge expressed in OSML. Includes example metabolic pathway, gene ontology, genome position, transcription and PPI knowledge in OSML format.

<This project has been completely rewrote and transformed into a new one: https://sourceforge.net/projects/deday/. 2013/06/26> The graphic user interface for DEDA (DEmography Data Analysis), a scientific software package fitting survivalship data to a number of distributions using maximum likelihood (ML) method. Currently, Weibull (2p), Gompertz and Gompertz-Makeham are supported. IMPORTANT NOTICE: Only the GUI is provided here. In order to perform the analysis, one also need the DEDA computation core program. Please email a request to me, entitled: 'Request for DEDA computation core', if you wish to have a copy.

Gxsm for Windows is the Windows version of the GXSM - Gnome X Scanning Microscopy, a complete open source software solution designed for Scanning Probe Microscopy-SPM techniques ( Scanning Tunneling Microscopy-STM, Scanning Force Microscopy-AFM...), but also SPA-LEED... The Windows version is up-to-date and keeps all the features as the Linux version as possible. Gxsm for Windows currently supports DSP hardware controller from Softdb such as SignalRanger SR1, SignalRanger SR2...

GEDAS is a software to perform microarray data analysis with friendly user interface and convenient data display. Currently some commonly used data clustering algorithms have been implemented in this software.

A module for JAGS containing several covariance functions for point-referenced data analysis and a function that creates the precision matrix for the proper CAR model for areal data analysis.

Ginkgo is a spotted microarray data pre-processing platform featuring analysis functionalities for CGH and expression data. [Pathogen Functional Genomics Resource Center (PFGRC) @ J. Craig Venter Institute (JCVI)]

GmanDA is a GPL software for performing qualitative data analysis on mailing-lists and mboxes. It was developed to ease the work with large scale mailing-list archives taken from Gmane.org

GnuTek analyses structural geology data. Data can be displayed in stereographic projections (Schmidt net) as great circles or pole points. Data analysis comprises counting of pole density, isoline figures and various 3-dim. statistics.

GA Beacon is a lightweight tracking proxy for pages that can display images but cannot run Google Analytics JavaScript. A page embeds a badge or transparent pixel whose URL identifies the analytics property and a meaningful tracking path. The service receives that image request, generates a visitor identifier, and forwards the hit through the Google Analytics Measurement Protocol. Cookies allow it to distinguish repeat visits without requiring client-side scripts. It can derive paths from referral data and offers several badge or pixel display modes. The public App Engine endpoint is intended mainly for demonstrations and prototypes. For production use, the repository is designed to be forked, customized, and deployed as a privately controlled Google App Engine service.