Open Source R Scientific/Engineering Software
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R Scientific/Engineering Software
View 200 business solutionsBrowse free open source R Scientific/Engineering Software and projects below. Use the toggles on the left to filter open source R Scientific/Engineering Software by OS, license, language, programming language, and project status.
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Application Monitoring That Won't Slow Your App DownFull APM with errors, performance, logs, and uptime monitoring. 99.999% uptime SLA on the platform itself.
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MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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Seurat
R toolkit for single cell genomics
Seurat is a comprehensive R toolkit for single-cell genomics analysis, introduced by the Satija Lab at NYGC. It supports quality control, normalization, clustering, integration of multimodal data (e.g., scRNA‑seq, spatial, CITE‑seq), and visualization. Seurat v5 introduces scalable workflows and spatial transcriptomics support, commonly used in academic and industry research for single-cell studies. -
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LabPlot
Data Visualization and Analysis
LabPlot is a FREE, open source and cross-platform Data Visualization and Analysis software accessible to everyone. -
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tidyverse
Easily install and load packages from the tidyverse
tidyverse is a meta‑package that installs and loads a cohesive suite of R packages designed for data science, sharing underlying design principles, grammar, and data structures. Core components include ggplot2, dplyr, tidyr, readr, purrr, tibble, stringr, forcats, and more. It promotes tidy data workflows and consistency across tasks. -
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broom
Convert statistical analysis objects from R into tidy format
broom is part of the tidymodels ecosystem that converts statistical model outputs (e.g. from lm, glm, t.test, lme4, etc.) into tidy tibbles — standardized data frames — using functions tidy(), glance(), and augment(). These are easier to manipulate, visualize, and report programmatically. -
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geocompr
Geocomputation with R: an open source book
This repository hosts the source for Geocomputation with R, an open-source book covering spatial data analysis, visualization, and modeling using R. It teaches how to work with vector and raster data, coordinate systems, mapping, and geocomputation techniques using packages like sf, terra, tmap, and more. Actively maintained and updated for real-world geospatial workflows. -
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MitoSAlt
Identification of mitochondrial structural alterations
MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided. -
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Amplicon_Sequencing_Worfklow
Analyzing amplicon data from sequences to stats
This is a collection of scripts and instructions on how to analyzing amplicon sequence data (i.e., 16S, ITS2, & other marker genes). I created this workflow to create a consistent set of methods for analyzing amplicon sequence data, from when you first receive the sequence data to statistical analyses & data visualization. All you need is to have the latest version of R installed, some experience with the command line & shell, and enough memory to run all of the programs. There are also instructions provided in case you are running these analyses via a computing cluster/Slurm workload manager. You can choose to go through the workflow using either an Rmd script, an html file, or a PDF, or via the homepage link provided. If you have questions or concerns, please don't hesitate to reach out. Thanks! -
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CausalImpact
An R package for causal inference in time series
The CausalImpact repository houses an R package that implements causal inference in time series using Bayesian structural time series models. Its goal is to estimate the effect of an intervention (e.g. a marketing campaign, policy change) on a time series outcome by predicting what would have happened in a counterfactual “no intervention” world. The package requires as input a response time series plus one or more control (covariate) time series that are assumed unaffected by the intervention, and it divides the time horizon into “pre-intervention” and “post-intervention” periods. It uses Bayesian modeling to fit a structural time series to the pre-period and extrapolate a counterfactual prediction for the post period, then compares observed vs predicted to infer the causal effect. The package supports plotting, summary tables, and verbal narratives for interpretive reports. -
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No-code system is for the visual creation of structural-functional models and the automatic generation of R language simulation models. The program can be used to describe information, production, organizational, and other processes. For graphical representation, the EdPM/EPM notation is used, which allowed us to implement: - structural-functional modeling using graphical methods; - the study of the efficiency of structural-functional models using simulation methods, that allow (e.g. unlike Petri nets) to process queries in groups, which is important for the study of the efficiency of using such methods as volumetric calendar planning and AI methods in process activities, since the operating time of these methods depends on the number of parameters and changes nonlinearly; - the study of multiprocess systems; - the results were obtained, that allow you to find efficient topologies of structural-functional models.
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Custom VMs From 1 to 96 vCPUs With 99.95% UptimeLive migration and automatic failover keep workloads online through maintenance. One free e2-micro VM every month.
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FAST-GHG
A fast tool to caculatate greenhouse gases in agriculture
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KidneyExplorer
Kidney proteomics data explorer enables you to investigate diseases
KidneyExplorer enables you to interactively survey kidney proteomics datasets from different kidney disease models. Here you can download the corresponding SQL database dumps. The original website for the shiny app is: https://kidneyapp.shinyapps.io/kidneyorganoids/ -
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OmicSelector
Feature selection and deep learning modeling for omic biomarker study
OmicSelector is an environment, Docker-based web application, and R package for biomarker signature selection (feature selection) from high-throughput experiments and others. It was initially developed for miRNA-seq (small RNA, smRNA-seq; hence the name was miRNAselector), RNA-seq and qPCR, but can be applied for every problem where numeric features should be selected to counteract overfitting of the models. Using our tool, you can choose features, like miRNAs, with the most significant diagnostic potential (based on the results of miRNA-seq, for validation in qPCR experiments). -
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Pain2D are programs which were developed for the automated pain drawing collection and classification of diseases on the basis of pain drawings in pen-and-paper and digital form for research purposes. Pain2D is currently not a diagnostic tool, but is aimed at scientists, physicians and anyone interested in the automated analysis of pain drawings.
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QuantifyPoly(A)
Quantification of poly(A) sites from 3' end sequencing data
QuantifyPoly(A) - a tool for quantification of poly(A) sites from 3' end sequencing data. [1] QuantifyPoly(A) user manual Please visit the Wiki page of this website. [2] QuantifyPoly(A) Q&A For Q&A, please visit the Blog page of this website. [3] QuantifyPoly(A) bug report You can report a bug as a Ticket request, or start a topic session in the Discussion webpage of this website. -
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Reproducible-research
A Reproducible Data Analysis Workflow with R Markdown, Git, Make, etc.
In this tutorial, we describe a workflow to ensure long-term reproducibility of R-based data analyses. The workflow leverages established tools and practices from software engineering. It combines the benefits of various open-source software tools including R Markdown, Git, Make, and Docker, whose interplay ensures seamless integration of version management, dynamic report generation conforming to various journal styles, and full cross-platform and long-term computational reproducibility. The workflow ensures meeting the primary goals that 1) the reporting of statistical results is consistent with the actual statistical results (dynamic report generation), 2) the analysis exactly reproduces at a later point in time even if the computing platform or software is changed (computational reproducibility), and 3) changes at any time (during development and post-publication) are tracked, tagged, and documented while earlier versions of both data and code remain accessible. -
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TOFSIMS
R/Bioconductor toolkit for mass spectrometry data
The tofsims project is an R/Bioconductor toolkit designed for processing, analyzing, and visualizing imaging mass spectrometry data from Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) instruments. It supports importing raw and preprocessed data from popular instrument platforms (e.g. IONTOF, Ulvac-Phi) and provides methods for mass calibration, peak picking, and peak integration. The package allows transformation of spectra into 2D image structures (mass images), with operations such as binning, scaling, subsetting, and visual rendering. For data exploration and dimensionality reduction, it includes multivariate methods common in the ToF-SIMS community: PCA (Principal Component Analysis), MCR (Multivariate Curve Resolution), MAF (Maximum Autocorrelation Factors), and MNF (Minimum Noise Fraction). It also interoperates with Bioconductor’s imaging stack (e.g. EBImage) so users can apply segmentation and image analysis operations on mass images. -
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Vascular prediction
Study develops predictive model to reduce 90-day readmissions.
In recent years, hospital readmissions have increased, affecting public evaluations and pay-for-performance measures. A study developed a predictive model for 90-day hospital readmission in patients undergoing elective vascular procedures. The best predictive model was Shrinkage Discriminant Analysis, which considered variables such as length of stay, comorbidity scores, procedure type, and admission type. The model indicates that efforts to reduce vascular readmissions should prioritize emergency procedures. This risk stratification allows for better identification and prevention of unnecessary readmissions, crucial in an environment where preventing unplanned readmissions is increasingly important. -
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miRPV
miRPV: An automated pipeline for miRNA Prediction and Validation in si
miRPV is an Automated tool that allows users to predict and validate microRNA from genome/gene sequence. System Requirement CPU: AMD64 (64bit) Memory: 2Gb RAM Storage: 5Gb Ubuntu 18.04 -
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osm4scala
Reading OpenStreetMap Pbf files.
Scala and polyglot Spark library (Scala, PySpark, SparkSQL, ... ) focused on reading OpenStreetMap Pbf files. -
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rethinking
Statistical Rethinking course and book package
This R package accompanies Richard McElreath’s Statistical Rethinking (2nd edition), offering utilities to fit and compare Bayesian models using both MAP estimation (quap) and Hamiltonian Monte Carlo via RStan (ulam). It supports specifying models via explicit distributional assumptions, providing flexibility for advanced statistical workflows. -
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yabasta
Yet Another BAsic Scraper and Text Analysis
YA BASTA! is a Python/R application for Lyrics Web Scraper and Text Analysis. Web scraping is developed in Python, text analysis in R as Python subprocesses. YA BASTA! is only tested on windows OS. To run YA BASTA! just type on window command prompt: python.exe yabasta.py
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