Open Source S/R Software for Linux

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  • 1
    iramuteq
    IRAMUTEQ : Interface de R pour les Analyses Multidimensionnelles de Textes et de Questionnaires. Logiciel de traitement de données pour des corpus texte ou de type individus/caractères. Permet notamment de réaliser des analyses de type "ALCESTE"
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    Downloads: 418 This Week
    Last Update:
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  • 2
    SimpleITK
    SimpleITK: a simplified layer build on top of the Insight Toolkit (ITK), intended to facilitate its use in rapid prototyping, education and interpreted languages.
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    2 Reviews
    Downloads: 77 This Week
    Last Update:
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  • 3
    R packages (maintained by YJLEE)

    R packages (maintained by YJLEE)

    R packages for PK/PD modeling , BE/BA, drug stability, ivivc, etc.

    These R packages are developed for data analysis of PK/PD modeling & simulation, bioequivalence/bioavailability (BE/BA), drug stability, in-vitro and in-vivo correlation (ivivc), as well as therapeutic drug monitoring (TDM).
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    3 Reviews
    Downloads: 57 This Week
    Last Update:
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  • 4

    PS Matching in SPSS

    Propensity score matching in SPSS

    Propensity score matching in SPSS Provides SPSS custom dialog to perform propensity score matching. Using the SPSS-R plugin, the software calls several R packages, mainly MatchIt and optmatch. Proper citations of these R packages is provided in the program.
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    2 Reviews
    Downloads: 57 This Week
    Last Update:
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  • 5
    gVirtualXRay

    gVirtualXRay

    Virtual X-Ray Imaging Library on GPU

    gVirtualXRay is a C++ library to simulate X-ray imaging. It is based on the Beer-Lambert law to compute the absorption of light (i.e. photons) by 3D objects (here polygon meshes). It is implemented on the graphics processing unit (GPU) using the OpenGL Shading Language (GLSL). SimpleGVXR is a smaller library build on the top of gVirtualXRay. It provides wrappers to Python, R, Ruby, Tcl, C#, Java, and GNU Octave.
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    5 Reviews
    Downloads: 11 This Week
    Last Update:
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  • 6
    mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
    Downloads: 15 This Week
    Last Update:
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  • 7
    TXM

    TXM

    Unicode XML TEI text analysis platform

    TXM is a free and open-source cross-platform Unicode & XML based text analysis environment and graphical client, supporting Windows, Linux and Mac OS X. It can also be used online as a J2EE standard compliant web portal (GWT based) with access control built in. DOWNLOAD LATEST VERSION OF TXM : http://textometrie.ens-lyon.fr/spip.php?rubrique61&lang=en TXM offers a comprehensive range of analysis tools (concordances, collocate search, frequency lists, etc.) based on the powerfull CQP full text search engine (http://cwb.sourceforge.net) and a range of statistical functions (factorial analysis, classification, cooccurrency analysis, etc.) based on R packages (http://www.r-project.org). Read the scientific background at the Textométrie project web site http://textometrie.ens-lyon.fr/?lang=en. Read a full description at the TEI Tools wiki http://wiki.tei-c.org/index.php/TXM.
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    Downloads: 10 This Week
    Last Update:
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  • 8
    Bio7
    The application Bio7 is an integrated development environment for ecological modelling and contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.
    Downloads: 8 This Week
    Last Update:
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  • 9
    Splicing Prediction Pipeline

    Splicing Prediction Pipeline

    Splicing Prediction Pipeline or SPiP

    SPiP is a tool to predict the splice alteration of variant by integrate several prediction tool in a global pipeline. You can also download SPiP in zip format: https://sourceforge.net/projects/splicing-prediction-pipeline/files/SPiP_alone_v2_1.zip For Linux (GitHub): https://github.com/LBGC-CFB/SPiP If you have questions, please contact me to: r.leman@baclesse.unicancer.fr or raphael.leman@orange.fr v2.1 corrected (07/2021) : correction of score calculation v2.1 (06/2021): Most strigent on "Alter by complex event" v2.0 (04/2021): New SPiP with random forest modelization old change detailled in https://sourceforge.net/projects/splicing-prediction-pipeline/files/changeLogBeforev2.0.txt
    Downloads: 8 This Week
    Last Update:
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  • 10

    libirt

    The new site is at http://psychometricon.net/libirt/

    The new site is at http://psychometricon.net/libirt/ Library of functions to estimate the items and abilities from the responses of subjects to a questionnaire. The IRT models supported are the logistic model, the multivariate logistic model, the graded model and smoothing by penalization and kernel.
    Downloads: 7 This Week
    Last Update:
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  • 11
    We are developing data standards and software tools that implement these standards to develop a systemic approach to modeling, capturing, analyzing and disseminating flow cytometry data.
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    2 Reviews
    Downloads: 2 This Week
    Last Update:
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  • 12
    MVSE

    MVSE

    Estimator of climate-driven, mosquito-borne viral suitability index

    Understanding how climate dictates the timing and potential of mosquito-borne viral transmission is essential for preparedness of public health systems and design of control strategies. We developed the Mosquito-borne Viral Suitability Estimator (MVSE) software package for the R programming environment. The package estimates a suitability index based on a climate-driven mathematical expression for the basic reproductive number (R0). By accounting for local climatic variables, as well as viral, vector and human priors, suitability can be estimated for specific regions, hosts, vectors and viral species. MVSE v0.3 and v1.01r are available for download in this repo. UPDATE Oct/2021: note that a correction has been made to the documentation of v1.01r. The most recent version is the file "MVSE_v1.01r_corrections_to_documentation.zip". No changes have been made to the code itself. Article for original v0.3: https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.132
    Downloads: 4 This Week
    Last Update:
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  • 13
    Mass-Up

    Mass-Up

    MALDI-TOF data analysis tool

    Mass-Up is an Open-Source mass spectrometry utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data. Mass-Up includes several tools and operations to load, preprocess and analyze MALDI-TOF data.
    Downloads: 4 This Week
    Last Update:
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  • 14

    bootf2BCA

    computing f2 bootstrap CI BCA

    Computing similarity factor (f2) bootstrap bias corrected and accelerated confidence interval
    Downloads: 4 This Week
    Last Update:
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  • 15
    We developed a systematic algorithmic solution for quantitative drug sensitivity scoring (DSS), based on continuous modeling and integration of multiple dose-response relationships in high-throughput compound testing studies. License: The DSS R-package is made available under the terms of the GNU General Public License, which means that the source code is freely available for use within other software, but if you alter the code and distribute it, you must make the new source code freely available as well. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. In case you use the package in your work, we do appreciate a citation to a DSS publication. Citation: Yadav et al. (2014), Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies. Scientific Reports 4, 5193; DOI:10.1038/srep05193 Please visit the link below for details
    Downloads: 2 This Week
    Last Update:
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  • 16
    The Life Cycle Assessment Spreadsheet allows you to calculate carbon footprints and other environmental impacts for given product systems. Use requires basic skills in LCA and matrix algebra, but rewards effort with professional analytical tools.
    Downloads: 2 This Week
    Last Update:
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  • 17
    NanoR

    NanoR

    R package built to analyze and compare Nanopore data

    NanoR is a package for the statistical language and environment R, tested on Unix, MacOSX and Windows, that allows user-friendly analysis and comparison of 1D MinION and GridION X5 sequencing data within acceptable time frames.
    Downloads: 2 This Week
    Last Update:
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  • 18
    OxyWitleaf2CSV

    OxyWitleaf2CSV

    Witleaf pulse oxymeter BIN format data decoder.

    The simple program is a Witleaf handheld pulse oxymeter BIN file format data decoder. It reads BIN-files produced by popular professional pulse oxymeters manufactured by Shenzhen Witleaf Medical Electronics Co., Ltd. (like the WIT-S300 shown in the photo on the project icon) and produces a CSV-formatted output with the extracted data to stdout (gets printed to the console if not directed otherwise). More info on https://github.com/mrKirushko/OxyWitleaf2CSV .
    Downloads: 2 This Week
    Last Update:
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  • 19

    PyRate

    Bayesian Estimation of Speciation and Extinction from Fossil Data

    PyRate is a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework. The method was described by D Silvestro, J Schnitzler, LH Liow, A Antonelli, and N Salamin in Systematic Biology (http://sysbio.oxfordjournals.org/content/early/2014/02/08/sysbio.syu006.abstract). *Please download the most up-to-date code from the "PyRate code" tab on this page or from: https://github.com/dsilvestro/PyRate * *An updated manual can be found here: https://github.com/dsilvestro/PyRate/tree/master/tutorials *
    Downloads: 2 This Week
    Last Update:
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  • 20
    Xpose - an S/R based population PK/PD model building aid for NONMEM.
    Downloads: 2 This Week
    Last Update:
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  • 21
    ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumors using Expression data) is a new approach to use gene expression signature to infer the fraction of stromal and immune cells in tumor tissues.
    Downloads: 2 This Week
    Last Update:
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  • 22
    An R package for metrology. metRology provides classes and calculation and plotting functions for metrology applications, including measurement uncertainty estimation and (eventually) inter-laboratory metrology comparison studies.
    Downloads: 2 This Week
    Last Update:
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  • 23
    CanReg5 (moved to Github)

    CanReg5 (moved to Github)

    Canreg5 is a software package for population based cancer registries

    Cancer registries need a tool to input, store, check and analyse their data. If these data are also coded and verified in a standard way, it facilitates the production of comparable analyses across registry populations. The main goal of the CanReg5 project is to provide a flexible and easy to use tool to accomplish these objectives. CanReg5 is a multi user, multi platform, open source tool to input, store, check and analyse cancer registry data. It has modules to do: data entry, quality control, consistency checks and basic analysis of the data It was designed with an emphasis on user friendliness, it has a modern user interface and is easy to navigate. Is available in several languages. (English, French, Spanish, Portuguese, Russian, Turkish, Georgian, and Chinese.)
    1 Review
    Downloads: 1 This Week
    Last Update:
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  • 24

    IQuant

    A pipeline for quantitative proteomics based upon isobaric tags

    IQuant is an automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification. IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system. This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. If you have any question about IQuant, please contact me: wenbo@genomics.cn. The source code of IQuant can be found here "https://sourceforge.net/p/iquant/code/".
    1 Review
    Downloads: 1 This Week
    Last Update:
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  • 25

    Waterloo

    Java-based scientific graphics

    Java-based scientific graphics with support for Java, Groovy, MATLAB, Python, the R statistical environment, Scala and SciLab.
    1 Review
    Downloads: 1 This Week
    Last Update:
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