Software
The Girke lab develops open-source software for data-intensive research in genome biology, chemical genomics, and bioinformatics. The repositories below highlight selected tools for drug discovery, spatial omics visualization, and scalable workflow-based analysis.
Drug Discovery and Chemical Informatics
This area includes software for chemical similarity searching, bioactivity analysis, compound-target mapping, and related cheminformatics applications in small-molecule discovery.
signatureSearch
Tools for gene expression signature analysis and the discovery of related perturbagens, compounds, and biological mechanisms, with companion data resources provided through the associated signatureSearchData package.
drugTargetInteractions
Software for identifying and analyzing compound-target interaction relationships in support of computational drug discovery.
bioassayR
Infrastructure for storing, querying, and analyzing large bioassay datasets within the R environment.
ChemmineR
Cheminformatics toolkit for compound similarity analysis, clustering, visualization, and structure-based data mining in R.
ChemmineOB
Interface connecting ChemmineR workflows to Open Babel functionality for broader structure processing and cheminformatics tasks.
fmcsR
Tools for fast maximum common substructure analysis to support compound comparison and chemical similarity workflows.
eiR
Software for structure-based compound similarity and search workflows using atom environment descriptors.
Spatial Omics Visualization
This software area focuses on interactive and publication-oriented visualization methods for spatially resolved omics datasets.
spatialHeatmap
Visualization toolkit for exploring spatially resolved omics data in anatomical and tissue-based contexts.
Large-Scale Data Analysis Workflows
These repositories provide scalable workflow infrastructure for reproducible analysis of large omics datasets across local, server, and high-performance computing environments.
systemPipeR
Workflow management environment for designing, running, monitoring, and documenting reproducible omics analysis pipelines.
systemPipeRdata
Companion package providing workflow templates, example datasets, and supporting resources for systemPipeR-based analyses.
systemPipeShiny
Web-based interface for interactive execution, management, and monitoring of systemPipeR workflows.
Workflow Templates
Collection of reusable workflow templates for common omics applications, designed to support reproducible and scalable data analysis with systemPipeR.