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Showing 16 open source projects for "research"
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workflowr
Organize your project into a research website
workflowr is an R package that helps researchers organize, version, and share their data science projects in a reproducible and transparent manner. It combines R Markdown, Git, and a structured file system to create a research website that tracks analysis, results, and code changes over time. It’s ideal for academic and collaborative research workflows. -
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Seurat
R toolkit for single cell genomics
...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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knitr
A general-purpose tool for dynamic report generation in R
knitr is an R package that acts as a literate programming engine, combining code execution and document generation. It executes code embedded in Markdown, LaTeX, or other formats and produces output with results interleaved into final documents. It powers R Markdown and supports caching, chunk options, graphics, and extensibility for reproducible analysis. -
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rollama
Wrap the Ollama API, which allows you to run different LLMs
...It is designed to make LLM usage accessible to data scientists and researchers who work primarily in R, allowing them to generate text, analyze data, and create embeddings without relying on external cloud services. The package emphasizes reproducibility and privacy by enabling local execution of models, which is especially valuable for sensitive or research-oriented workflows. It supports common LLM tasks such as text generation, annotation, and embedding creation, making it useful for tasks like document analysis and data labeling. The design mirrors familiar R workflows, allowing users to integrate AI capabilities into scripts, notebooks, and data pipelines with minimal friction. ... -
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Glycometrics
Algorithms for glycaemic variability
Glycometrics is a collection of algorithms that provide metrics for glycaemic variability. Its application is mainly in theoretical endocrinology and diabetes research. -
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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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MetEx
MetEx is a computational tool for metabolite targered extraction and a
Liquid chromatography–high resolution mass spectrometry (LC-HRMS) is the most popular platform for untargeted metabolomics methods, but annotating LC-HRMS data is a long-standing bottleneck that we are facing since years ago in metabolomics research. A wide variety of methods have been established to deal with the annotation issue. To date, however, there is a scarcity of efficient, systematic, and easy-to-handle tools that are tailored for metabolomics and exposome community. So we developed a user-friendly and powerful software/webserver, MetEx, to both enable implementation of classical peak detection-based annotation and a new annotation method based on targeted extraction algorithms. ... -
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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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Covidex
Ultra fast and accurate subtyping tool of viral genomes.
Viral subtypes or clades represent clusters among isolates from the global population of a defined species. Subtypification is relevant for studies on virus epidemiology, evolution and pathogenesis. In this sense, Covidex was developed as an open source alignment-free machine learning subtyping tool. It is a shiny app that allows fast and accurate classification of viral genomes in pre-defined clusters. If more than 1000 sequences are loaded the tool will run in multithread mode. Capable of... -
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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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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covid19model
Code for modelling estimated deaths and cases for COVID19
Code for modeling estimated deaths and infections for COVID-19 from "Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe", Flaxman, Mishra, Gandy et al, Nature, 2020, the published version of our original Report 13. This is the release related to our Tiers paper, where we use the latent factor model to estimate the effectiveness of tiers systems in England. Peer-reviewed version is to be out soon. All other code is still the same for previous releases. The code... -
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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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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.... -
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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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Data Science Specialization
Course materials for the Data Science Specialization on Coursera
The Data Science Specialization Courses repository is a collection of materials that support the Johns Hopkins University Data Science Specialization on Coursera. It contains the source code and resources used throughout the specialization’s courses, covering a broad range of data science concepts and techniques. The repository is designed as a shared space for code examples, datasets, and instructional materials, helping learners follow along with lectures and assignments. It spans... -
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RStan
RStan, the R interface to Stan
...Key inference approaches include full Bayesian inference via Hamiltonian Monte Carlo (specifically the No-U-Turn Sampler, NUTS), approximate Bayesian inference via variational methods, and optimization (penalized likelihood). RStan integrates with Stan’s automatic differentiation library, provides diagnostics, model comparison, posterior predictive checks, etc. It is used in research, applied statistics, and modelling workflows where flexibility and rigor in Bayesian methods are required.
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