Software and Resources

R/Bioconductor packages

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

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

Data resources

These are data packages that I created or contributed to:

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

    • Explore interactively Transcriptome 3’end diversification (TREND)
    • An interactive web application to explore transcriptome signatures of heart failure
    • The iSEE COVID Hub
    • The iSEE portal for the HCA Tonsil Atlas
    • 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:

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

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