Marcel Ramos

The paper provides an open-source online book for analyzing spatial transcriptomics data using Bioconductor in R, with reproducible code and datasets.

The paper introduces an open-source ecosystem for microbiome data science using Bioconductor, supporting modular workflows for analyzing complex, multi-modal datasets.

The paper benchmarks differential abundance methods using microbiome datasets with known biological ground truth, finding that compositional methods are less effective than commonly used non-compositional approaches.

bamSliceR enables rapid, cross-cohort variant analysis by extracting and analyzing aligned reads from GDC data, identifying clinically relevant variants in leukemia cohorts.

The paper provides a Bioconductor package with curated landmark datasets for single-cell multimodal data, enabling easy access and analysis of seven different technologies.

The paper describes AnVIL, a cloud-based platform that enables genomic data analysis without data transfer, improving security, scalability, and collaboration.

GenomicSuperSignature compares new RNA-seq datasets to public archives for rapid interpretation using precomputed axes of variation.

HGNChelper identifies and corrects invalid gene symbols in human and mouse data by leveraging authoritative databases and addressing spreadsheet-related errors.

The paper benchmarks gene set enrichment methods using a curated compendium of disease datasets, identifying performance differences and providing recommendations for improved analysis.

HMP16SData provides integrated 16S rRNA sequencing data from the Human Microbiome Project, enabling easier analysis for researchers with basic R skills.

The paper introduces curatedMetagenomicData, a resource providing curated metagenomic profiles for analysis in R with minimal bioinformatic expertise.

The paper introduces MultiAssayExperiment, a Bioconductor package for integrating multi-omics data, demonstrating its use with TCGA datasets to simplify analysis and visualization.