Vignettes

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.