Search Results for "data integration"

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.

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 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. ...