Erick Lu

single-cell-rnaseq-analysis

Website · GitHub

A guide for analyzing single-cell RNA-seq data using the R package Seurat. Go from raw data to cell clustering, identifying cell types, custom visualizations, and group-wise analysis of tumor infiltrating immune cells using data from Ishizuka et al. Nature 2019.

bulk-rnaseq-analysis

Website · GitHub

A complete guide for analyzing bulk RNA-seq data. Go from raw FASTQ files to mapping reads using STAR and differential gene expression analysis using DESeq2, using example data from Guo et al. 2019.

python-fastq-downloader

Website · GitHub

A guide on how to find and download raw RNA-seq data from GEO. Batch download FASTQ files using a Python script and the NCBI SRA tools prefetch and fastq-dump.

dendritic-cell-bulk-rnaseq

Website · GitHub

Analyze bulk RNA-seq data from Li et al. 2016 to identify upregulated genes in activated dendritic cells.

cell-line-transcriptome-analysis

Website · GitHub

Use R to clean and analyze RNA-seq data from 64 cell lines from The Human Protein Atlas and identify differentially expressed genes.

pubmed-abstract-compiler

Website · GitHub

Python script that downloads all pubmed abstracts corresponding to user-specified keyword searches, by performing automated NCBI E-utility queries

gene-expression-databases

Website · GitHub

A compilation of public databases for determining gene expression patterns and survival associations. No coding required!

IHC-image-pixel-analyzer

GitHub

Use Matlab to break an image into blocks and export properties for each block. Then use R to analyze the output.

R-for-data-science-walkthrough

Website · GitHub

A walkthrough of Hadley Wickham and Garrett Grolemund's book, R for data science (r4ds), with my solutions to their exercises and some of my own notes and data explorations.

web-scraping-NBA-statistics

Website · GitHub

Use Python to scrape ESPN for stats on all players in the NBA. Obtain and organize data, calculate statistics, and model using urllib, re, pandas, and scikit-learn.

cancer-publication-time-series

Website · GitHub

Model the number of cancer papers published over time and visualize the data using the TSA package in R.