AtlasLens is developed, an open-source R/Shiny application for interactive exploration of scRNA-seq datasets and integrated cellular atlases that integrates interactive visualization, differential expression analysis, Gene Ontology enrichment with redundancy reduction, temporal expression analysis, and context-dependent gene function profiling through GeneCOCOA.
Abstract
Motivation The rapid expansion of single-cell RNA sequencing (scRNA-seq) atlases has generated datasets comprising millions of cells annotated with increasingly rich metadata, including tissue, cell type, disease status, sex, age, treatment, and temporal information. Biological questions frequently require simultaneous interrogation of multiple metadata dimensions, such as identifying specific cell populations within defined tissues, disease states, demographic groups, and time points. While existing interactive platforms facilitate visualization and analysis of scRNA-seq data, deep metadata-driven exploration and downstream analysis of atlas-scale datasets remain insufficiently supported. Results We developed AtlasLens, an open-source R/Shiny application for interactive exploration of scRNA-seq datasets and integrated cellular atlases. AtlasLens enables iterative filtering across arbitrary metadata combinations, allowing users to define biologically meaningful cellular subsets and immediately perform downstream analyses. The platform integrates interactive visualization, differential expression analysis, Gene Ontology enrichment with redundancy reduction, temporal expression analysis, and context-dependent gene function profiling through GeneCOCOA. AtlasLens additionally records analysis history and automatically generates corresponding R code to enhance reproducibility. The application is distributed through Docker for simple local deployment, preserving data privacy and eliminating dependency-management challenges. We demonstrate AtlasLens using the Tabula Muris and a time-resolved whole-lung single-cell atlas of bleomycin-induced lung injury and fibrosis, highlighting its ability to support complex metadata-driven biological investigations. Availability Source code is available at https://github.com/SchulzLab/AtlasLens. Contact marcel.schulz@em.uni-frankfurt.de
Knowledge of RNA sequences, expression, splicing, isoforms, structure and modifications is central for understanding and targeting cellular processes. Revolutionary single-cell and spatial transcriptomics technologies-for example, as deployed by consortia such as the Human Cell Atlas-partially capture this diversity and generate cellular profiles that expand at petabyte scale each year1-5. Yet researchers cannot search sequences across these datasets: standard pipelines do not scale or rely on references, retaining only gene or isoform counts, whereas accessing raw sequences requires collecting, downloading and processing millions of large files. Here we present Malva, a computational platform that enables ultrafast, species-agnostic and reference-free interrogation of the raw sequence space, enabling searching for any sequence, mutation, splice junction or pathogen, or spatial location of arbitrary transcripts. The continuously expanding Malva Index currently comprises around 74 million cells from thousands of experiments in health and disease. Malva enables reference-free discovery-researchers can, for example, identify cell types and predict cell-cell similarity directly from sequence composition. Building on Malva's speed and accuracy, we demonstrate how Malva can be flexibly connected to state-of-the-art neural networks and how to execute complex searches and enable automated analyses. Malva transforms single-cell atlases from static gene count tables into dynamic, sequence-resolved resources that may help to bridge human-machine reasoning about biology.
D. León-Periñán, Nikos Karaiskos, N. Rajewsky· Nature· 0 citations
Bulk and single-cell RNA sequencing (scRNA-seq) have become essential for investigating disease mechanisms and identifying diagnostic biomarkers. However, the growing volume of transcriptomic data remains difficult to reuse efficiently for many researchers. Downstream analysis often requires multiple statistical, visualization, and reporting tools, creating fragmented workflows that reduce transparency and reproducibility, particularly when analyzing scRNA-seq data. To address this gap, we developed CoTRA (Comprehensive Toolbox for RNA-seq Analysis), an open-source R/Shiny package for bulk and scRNA analysis. CoTRA integrates established methods into modular workflows, exposes parameters, and offers alternatives at selected stages. It supports bulk RNA-seq quality assessment, differential expression, annotation, enrichment, and reporting, as well as scRNA quality control, dimensionality reduction, clustering, marker identification, cell-type annotation, differential abundance, trajectory inference, pathway activity, and cell-cell communication. CoTRA runs on workstations or HPC environments without mandatory external data submission and was tested on Linux, Windows, and macOS. Compared with 14 other platforms for bulk RNA-seq/scRNA-seq, CoTRA supported 46 of 49 predefined functionality criteria. Tool validation using published rd10 retinal bulk RNA-seq identified 1,947 shared differentially expressed genes with concordant direction and strong log2 fold-change agreement. A retinal scRNA-seq case study demonstrated appropriate clustering, cell-type resolved analysis, and pathway activity scoring. CoTRA provides a graphical environment for bulk and single-cell RNA-seq analysis while retaining parameter transparency, methodological flexibility, and reproducible outputs. Strong concordance with the published bulk RNA-seq analysis supports the workflow consistency, while the single-cell case study demonstrates its applicability to advanced scRNA-seq analysis. The source code is freely available at https://github.com/UmairSeemab/CoTRA.
Spatial transcriptomics (ST) profiles genome-wide gene expression while preserving the two-dimensional spatial context of mRNA molecules within tissue sections, enabling studies of tissue architecture and microenvironment-associated biology. However, ST analysis remains challenging because data import, quality control, integration, deconvolution, spatial statistics, and visualization often require multiple software environments and reproducible parameter choices. This protocol presents a practical computational workflow for public ST datasets in R, beginning with data acquisition and software setup and proceeding through Seurat-based data loading, quality control, normalization, multi-sample integration, clustering, and spatially variable gene analysis. The workflow then applies complementary deconvolution strategies, including reference-guided SPOTlight analysis and unsupervised STdeconvolve topic modeling, followed by Giotto-based spatial cell-cell communication analysis and interactive region-of-interest (ROI) selection using a custom Python Dash application. By emphasizing script-based execution, explicit parameter rationales, expected outputs, and troubleshooting checkpoints, the protocol provides an adaptable framework for standard array-based ST datasets and related platforms after dataset- and platform-specific parameter evaluation.
Hua-Lin Wang, Weijia Chen, Yan Wu et al.· Journal of Visualized Experi...· 0 citations
GEOMeta provides a scalable resource and reproducible framework for metadata curation in the Gene Expression Omnibus, and benchmarked transcriptome representation models for predicting sex, age, tissue and disease from transcriptome embeddings.
Xiaodan Zhang, S. Paithankar, Jing Pu et al.· bioRxiv· 0 citations
Spatial-transcriptomics integrates high-dimensional single-cell data with microscopy to reveal cellular states, communication, and tissue organization. Analyzing this data requires a combination of multi-modal data processing, high-dimensional data analysis, spatial analysis, and integrated visualization. However, computational analysis is increasingly becoming a bottleneck as approaches mature and dataset sizes increase. Additionally, visualization can be challenging as open-source visualization tools struggle to scale to large datasets (exceeding 1 billion transcripts), and commercial visualization tools are costly, closed source, and inflexible. We present Celldega, an open-source Python and JavaScript library for scalable, interactive visualization and analysis of spatial-omics data. Celldega integrates custom analyses, performs neighborhood analysis, implements an efficient visualization-specific file format, and enables interactive exploration in notebooks and web galleries. We demonstrate Celldega across multiple technologies, tissues, and datasets, including 3D reconstructions of the developing whole mouse head comprising over four million cells. Finally, we demonstrate how Celldega can be utilized throughout the entire lifecycle of spatial data analysis, from quality control to building a public shareable gallery.
Nicolas F. Fernandez, Jaspreet Ishar, Huan Wang et al.· bioRxiv· 0 citations
MKMC (Multi-sample Kmer Counter), a scalable, reference-free toolkit for RNA-seq analysis that leverages k-mer–based statistics to detect biological variation without requiring alignment, is presented.
L. Mboning, Maciej Dlugosz, Marek Kokot et al.· bioRxiv· 0 citations