My research and development work has resulted in various software packages, primarily focused on bioinformatics and data visualisation.
iSEE Ecosystem
The iSEE (Interactive SummarizedExperiment Explorer) ecosystem provides a framework for interactive visualisation of genomics data.
I have collaboratively developed and maintain the core iSEE package along with several extension packages in the Bioconductor project.
iSEE
Core framework for interactive visualisation of genomics data.
iSEEindex
Portal for multiple data sets in a single interface.
iSEEde
Differential expression visualisation panels.
iSEEpathways
Pathway analysis visualisation panels.
iSEEhex
Panels specialised in hexagonal binning.
iSEEhub
Portal for the Bioconductor ExperimentHub data resources.
iSEEu
The “iSEE universe”. Goal: a wrapper for all iSEE extensions, like the tidyverse. For now, a collection of miscellaneous panels and “modes”.
For more information and links to third-party extensions, please visit the iSEE website.
Other Bioconductor Packages
Other software packages I have developed and maintain in the Bioconductor project include:
velociraptor
A tool for the analysis of RNA velocity in single-cell RNA-seq data.
TVTB
The VCF Tool Box for genetic variation data.
GOexpress
Gene expression patterns with GO annotations.
Bioconductor Contributions
Bioconductor packages to which I have contributed code, documentation, or other improvements.
BiocCheck
A package for checking Bioconductor package compliance.
Other Contributions
Panpipes
Multi-modal single cell analysis pipelines.
Comprehensive workflows for scRNA-seq, CITE-seq, scV(D)J-seq, scATAC-seq, and spatial transcriptomics
Pet Projects
Personal software experiments and tools available on GitHub.
deeperTools
R package to process files produced by deepTools.
sqlighter
R package providing wrapper functions around the RSQLite package.
hancock
R package for learning and applying gene signatures associated with cellular phenotypes and identities.
unisets
R package providing S4 classes to store relationships between elements and sets, with a particular emphasis on gene sets.
