Software and Resources

R/Bioconductor packages

I am a maintainer or contributor of the following R packages:

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  • A toolkit to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
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  • Interactive Visualization of RNA-seq Data Using a Principal Components Approach
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  • Interactive Differential Expression AnaLysis, to extract quickly and effectively information downstream the step of differential expression.
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  • A package for enjoying transcriptomic data and analysis responsibly - like sipping a cocktail, where expression matrix, DE results, enrichment results are all seamlessly combined
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  • The interactive SummarizedExperiment Explorer
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  • The iSEE Universe
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  • iSEE extension for panels related to differential expression analysis
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  • iSEE extension for panels related to pathway analysis
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  • iSEE for the Bioconductor ExperimentHub
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  • iSEE extension for a landing page to a custom collection of data sets
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  • Graphical Exploration of Design Matrices
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  • Quantification of the Tumor Immune contexture from RNA-seq data
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  • Estimate Systems Immune Response from RNA-seq data
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  • Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics
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  • Simulate Bulk RNA-seq Datasets from Single-Cell Datasets
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  • A better way to explore what is best
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  • The Geneset Distances project
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  • MOStly used Differential Expression Functions
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  • Implementation of a single cell allele experiment class
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  • An interface to HUBMAP, to explore the Human BioMolecular Atlas Program Data Portal
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  • Streamlining the creation of initial states for starting an iSEE instance

Data resources

These are data packages that I created or contributed to:

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  • Accessing The Datasets Of The Human Cell Atlas in R/Bioconductor
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  • Bulk and single-cell RNA-seq data from the Tabula Muris Senis project
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  • easier internal data and exemplary dataset from IMvigor210CoreBiologies package
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  • Provides programmatic access to the tonsil cell atlas datasets
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  • A data package for the SingleCellAlleleExperiment class and data type

Web applications

I also developed some web applications and dashboards for data analysis and exploration:

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  • Explore interactively Transcriptome 3’end diversification (TREND)
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  • An interactive web application to explore transcriptome signatures of heart failure
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  • The iSEE COVID Hub
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  • The iSEE portal for the HCA Tonsil Atlas
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  • iSEE for the manuscript “Myeloid cell coagulation factor Xa-protease activated receptor 2 signaling inhibition expands progenitor exhausted T-cells in the tumor microenvironment”

Other software packages

These are some software packages, currently on Github, that I developed or contributed to:

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  • Simulation of recurrent event data in the total time model
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  • Filter and prioritize fusion calls
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  • Data package for annoFuse
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  • An R package for comparing sessionInfos in a smooth way
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  • Package/Shiny App for the omnideconv package
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  • A user-friendly framework for the visual comparison of two or more results from Differential Expression Analysis workflows
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  • A a tool for planning sample sizes in different experimental designs
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  • Power and sample size calculation in mixed model settings, with a focus on stepped wedge designs
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  • The one-stop shop for retrieving, accessing, and using network data in R/Bioconductor
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  • Quantification of the single cell immunogenomic diversity
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  • A collection of functions commonly used by members of the IMBEI

Other resources

Here you can find a list of other resources I contributed to (e.g., accompanying manuscripts):

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  • The Orchestrating Single Cell Analysis (OSCA) book, available at https://bioconductor.org/books/devel/OSCA/
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  • A curated list of software and resources for exploring and visualizing (browsing) expression data
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  • Stickers for some Bioconductor packages
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  • A gallery-repository to store the commands to reproduce entire analyses for iSEE instances on public/own data
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  • Supplementary Information for the ideal manuscript
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  • Supplementary Information for the GeneTonic manuscript
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  • Repository for the protocols included in the manuscript “Interactive and reproducible workflows for exploring and modeling RNA-seq data with pcaExplorer, ideal, and GeneTonic”.
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  • Source codes for the analyses of the MAGNet RNA-seq dataset, available via the Magnetique application
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  • Repository for the publication “Unraveling the Glycosphingolipid Metabolism Leveraging Transcriptome-weighted Network Analysis on Neuroblastic Tumors”