An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

Jupyter Notebook / Voila App for analysis and filtering of RNA-Seq data for clinical genetics diagnostics

GenePattern Notebook running Kallisto

Workspace for data science projects and NGS pipelines. Contains RStudio, Jupyter Notebook, VSCode and file manager. Can connect to Tailscale network to bypass firewalls.

Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.

This series of Jupyter Notebooks will guide users through using various tools and programs to analyze experimental groups

Data science project work with genomics/biological data

This is the bioinformatics workflow notebook for the analysis of wet lab-derived Candida albicans RNA-seq samples for BIOL 379.

All notebooks for data processing and visualization in Lu et al., Glutamine dependent signaling controls pluripotent stem cell fate. Developmental Cell (2022) https://doi.org/10.1016/j.devcel.2022.02.003