Notebooks documenting common experimental and bioinformatics workflows used in the Gresham Lab at NYU.
Rendered notebooks are available at https://greshamlab.bio.nyu.edu/vignettes/. Each .nb.html file embeds the source .Rmd, which can be downloaded directly from the website.
| Directory | Topic |
|---|---|
flow_cytometry/ |
Flow cytometry analysis with CytoExploreR (Cytek Aurora) |
growth_curves/ |
Growth curve analysis from Tecan plate reader data using Growthcurver |
reform/ |
Building custom genome and annotation files with reform |
nanopore_tools/ |
Nanopore basecalling (Guppy) and alignment (minimap2) on the HPC |
nanopore_cdna_isoforms/ |
cDNA isoform calling from Nanopore reads using ONT's Snakemake pipeline |
windchime/ |
Paired-end RNAseq with UMIs: trimming, STAR alignment, UMI-tools deduplication, and feature counts for DESeq2 |
ggplot/ |
Introduction to ggplot2 for data visualization |
tidyverse/ |
Introduction to tidy data and dplyr |
All vignettes are self-contained RMarkdown (.Rmd) notebooks. Supporting files (images, example data, config templates) are kept in the same subdirectory as their notebook. Reference files shared across vignettes are in data/.
Each vignette should be an html_notebook RMarkdown document. To render locally:
rmarkdown::render("vignette_dir/notebook.Rmd")Rendered .nb.html files are excluded from the repository via .gitignore.