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Erick Lu's Projects

abstract-date-parser icon abstract-date-parser

Takes a collection of PubMed abstracts and creates an equidistant time series of the number of papers published over time, using python/pandas.

bulk-rnaseq-analysis icon bulk-rnaseq-analysis

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.

erilu.github.io icon erilu.github.io

Modified the square.github.io website to turn it into a data analysis portfolio.

gene-expression-databases icon gene-expression-databases

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

ihc-image-pixel-analyzer icon ihc-image-pixel-analyzer

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

pubmed-abstract-compiler icon pubmed-abstract-compiler

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

python-fastq-downloader icon python-fastq-downloader

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.

r-for-data-science-walkthrough icon r-for-data-science-walkthrough

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.

single-cell-rnaseq-analysis icon single-cell-rnaseq-analysis

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.

web-scraping-nba-statistics icon web-scraping-nba-statistics

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.

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