Vignettes of computational workflows used in the lab.  All code is available on github.

Modify reference genome and annotation files our lab’s custom R package and the reform python script or web application.

Basecalling and aligning nanopore data on NYU HPC using slurm. 

             cDNA Isoform calling for Nanopore


The windchime pipeline for running RNAseq analysis using the lexogen kit with paired-end sequencing and UMI-based deduplication.

Examples of using ggplot to generate plots in R.

Demonstration of the use of tools in tidyverse to wrangle and explore data.

Growth curves

Analyzing 96 well Tecan plate reader data

Simple flow cytometry analysis using cytoExploreR

Lineage aware variant filtering using Heranca


VIVALDI – Viral Variant Location and Diversity