Open Source S/R Software - Page 5
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S/R Software
Browse free open source S/R Software and projects below. Use the toggles on the left to filter open source S/R Software by OS, license, language, programming language, and project status.
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Inventory and Order Management Software for Multichannel SellersWe are the most powerful inventory and order management platform for Amazon, Walmart, and multichannel product sellers. Centralize orders, product information, and fulfillment operations to run more efficiently, sell more products, and stay compliant with marketplace requirements so you can grow profitably.
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Agentic AI SRE built for Engineering and DevOps teams.NeuBird AI's agentic AI SRE delivers autonomous incident resolution, helping team cut MTTR up to 90% and reclaim engineering hours lost to troubleshooting.
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Toolchain for quantification of fluorescence intensity and morphological parameters in single cells using microscope based cytometry.
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Celsius is a data warehouse that provides web services for upload, archival, download, annotation, quantification, and normalization of all Affymetrix microarray platforms.
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Chinese I Ching R Algorithms
Chinese I Ching Algorithms implemented with R programming
I Ching offers an idea to summary the world by constructing functional mappings in finite groups. Much of ancient Chinese natural and social science grew from its concepts as root. The derived theories like "Eight Diagrams", "Five Elements" became the foundation of nearly all academic fields in acient Chinese. As a result, the theories are also the high concentration of many practical and statistical experience in China during her thousands-of-year history. This project tries to realize these algorithms with statistical programming. Overcoming the long span has important meanings. First, we can verify the validity of algorithm with big data. Second, we can put them into unprecedented wide application in the age of data. Third, the unique inspection of I Ching that linked "all the universe" open new eyes for us in thought and methodology about interdisciplinary use of data. This program is open-source for human. If you are interested in it, welcome to discuss and work together. -
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Chipster is a biologist-friendly analysis software for high-throughput data. It contains over 200 analysis tools for next generation sequencing (NGS), microarray and proteomics data. Users can combine tools in automatic analysis workflows, which can be shared. Chipster's interactive visualizations allow users to select datapoints and create new gene lists. For NGS data Chipster contains a built-in genome browser, which highlights SNPs and automatically indexes BAM files and calculates coverage. Chipster’s ability to provide a biologist-friendly access to a powerful analysis platform is technically based on a desktop application user interface, a flexible distributed architecture, and the ability to integrate many types of analysis tools (command line, R/Bioconductor, Java, Web Services etc). The platform is generic and easily extendable to other areas, even beyond bioinformatics. For more information, please see http://chipster.csc.fi and http://genomebiology.com/1471-2164/12/
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Next-Gen Encryption for Post-Quantum Security | CLEAR by Quantum KnightCLEAR by Quantum Knight is a FIPS-140-3 validated encryption SDK engineered for enterprises requiring top-tier security. Offering robust post-quantum cryptography, CLEAR secures files, streaming media, databases, and networks with ease across over 30 modern platforms. Its compact design, smaller than a single smartphone image, ensures maximum efficiency and low energy consumption.
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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.
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CoLabR
A simple user interface to the R software environment.
A simple user interface to the R software environment. It is designed for people new to R and provides the user with easy access to their variables and data along with pointers to the most basic commands. It also allows for multiple people to share data across different sessions on different machines. In this way it also offers a collaborative environment for people to work together in remote locations. -
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Community Detection Modularity Suite
Suite of community detection algorithms based on Modularity
- MixtureModel_v1r1: overlapping community algorithm [3], which includes novel partition density and fuzzy modularity metrics. - OpenMP versions of algorithms in [1] are available to download. - Main suite containing three community detection algorithms based on the Modularity measure containing: Geodesic and Random Walk edge Betweenness [1] and Spectral Modularity [2]. Collaborator: Theologos Kotsos. [1] M. Newman & M. Girvan, Physical Review, E 69 (026113), 2004. [2] M. Newman, Physical Review E, 74(3):036104, 2006. [3] B. Ball et al, An efficient and principled method for detecting communities in networks, 2011. The suite is based upon the fast community algorithm implemented by Aaron Clauset <aaron@cs.unm.edu>, Chris Moore, Mark Newman, and the R IGraph library Copyright (C) 2007 Gabor Csardi <csardi@rmki.kfki.hu>. It also makes of the classes available from Numerical Recipies 3rd Edition W. Press, S. Teukolsky, W. Vetterling, B. Flanne -
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ConDEnSE (Confidential Data Enabled Statistical Exploration) will be a web-based environment for statistical analysis of confidential data from various database sources, based on Plone and R, and using the Jackknife method of confidentiality protection.
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Corbata
CORe microBiome Analysis Tools
Corbata is a set of statistical tools that can be used to analyze the core microbiome across a set of samples. -
Premier Construction SoftwareRated #1 Construction Accounting Software by Forbes Advisor in 2022 & 2023. Our modern SAAS solution is designed to meet the needs of General Contractors, Developers/Owners, Homebuilders & Specialty Contractors.
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Cygwin Ports
Repository of desktops and programs for the Cygwin platform
A large repository of open-source programs built for Cygwin, including X11 desktops, language interpreters, multimedia frameworks, cross-compiler toolchains, and much more. Also hosted here is the cygport tool for building Cygwin packages. cygport releases and the Ports Git repositories are hosted here; Ports packages are available from the website. -
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DACAClus
Algoritmo divisivo de clustering.
Algoritmo divisivo de clustering con determinación automática de componentes. -
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DEAPathways
Differential Expression Analysis for Pathways
This project contains the source code associated with the PLoS Computational Biology publication: "Differential Expression Analysis for Pathways". The paper text can be found here: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002967 -
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DESN
Differential activE sub-Network (DEN): R/Bioconductor based package
Living cells are complex, dynamic, self-regulatory, interactive systems, showing differential states across time and space. Complexity of cellular systems is highlighted with the multi-layered regulatory mechanisms involving the interactions between bio-molecules (such as DNA, RNA, mi-RNA and proteins). These interactions are analyzed in the form of static networks. Likewise, number of experimental techniques like microarray, RNASeq allows quantification of cellular dynamics and aid in discerning differential gene expression across diverse conditions. Computational biology is in need of methods for integration of static networks and gene expression data, since it provides interesting insights into the dynamics of biological systems. DEN is an R/Bioconductor based package designed to assemble different types of human bio-molecular interactions as a complete interactome and contains functions to extract dynamic active networks by integration of gene expression data. -
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Deem
Analyze time-course data with significance tests, clustering, modeling
Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional currently. The app was and is developed at the University of Rochester (http://cbim.urmc.rochester.edu) under the GPL 3.0 license. This is a fork of that project. -
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Digital Expression on the Web
DEW is a platform that allows users to explore RNA-Seq data
DEW is a platform that allows users to explore RNA-Seq data. A web-based Graphical User Interface is included. The analysis proceeds as such: gapped alignments are performed and corrected for length, PCR and fragment bias so that a Fragment Per (effective) Kilobase per Million of reads (FPKM) is estimated as well as the simpler Reads Per Kb per Million of reads (RPKM). When provided with multiple isoforms and in the ‘contextual’ mode, corrections include a expectation maximization algorithm estimates effective expression profiles and a corrected alignment is produced. For each gene the user provides, DEW computes coverage descriptive statistics (RPKM, FKMP and total, mean and median corrected counts), expression profiles (normalized as R/FPKM and trimmed mean of fold change). DEW allows users to explore the data by providing interactive graphs. -
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Django-dataplot enables developers using the Django web framework to seamlessly integrate data-driven graphical plots into their web pages.
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DuffyRNAseq is an R package that implements an analysis pipeline for processing RNA-seq data from Illumina NextGen sequencers, to measure gene transcription and differential expression.
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A Python library bringing together utilities I've written over the years for work in bioinformatics and biostatistics, which should be generally applicable outside these fields as well. Focuses on string processing, DBI, and math.
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Electrophysiology & circular stats tools
Data analysis and circular statistics with OpenElectrophy and R
Set of tools for basic analysis of electrophysiological data. The Python classes show how to call OpenElectrophy functions and save data. The R library applies circular statistics to spike phase data and saves the best von Mises fit and the Rayleigh statistics on the disk. The wavelet coherence analysis is done in R by the package "sowas". Check the module R_coherence to see how we solved that problem. This packages may be useful for people who start using OpenElectrophy and circular statistics in R. If you find errors, please report them. The project is still in development, so in the future you'll get updates. -
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ElicitN
Interface for expert elicitation of numbers
ElicitN uses R and a tcltk gui interface for eliciting a number from an appropriate expert. The code has been modified from it's original version designed specifically for eliciting the number of species on coral reefs from expert taxonomists. For more information please refer to: http://dx.doi.org/10.1016/j.envsoft.2011.11.011 Please also refer to GitHub for a even simpler more recently maintained version of the project: https://github.com/beckyfisher/ElicitN -
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Ericscript is a computational framework to detect gene fusions from paired end RNA-seq data with high sensitity and specificity.
