Erick Lu's repositories
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.
pubmed-abstract-compiler
Python script that downloads all pubmed abstracts corresponding to user-specified keyword searches, by performing automated NCBI E-utility queries
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.
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.
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
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.
dendritic-cell-bulk-rnaseq
Analyze bulk RNA-seq data from Li et al. 2016 to identify upregulated genes in activated dendritic cells.
cell-line-transcriptome-analysis
Use R to clean and analyze RNA-seq data from 64 cell lines from The Human Protein Atlas and identify differentially expressed genes.
gene-expression-databases
A compilation of public databases for determining gene expression patterns and survival associations. No coding required!
cancer-publication-time-series
Model the number of cancer papers published over time and visualize the data using the TSA package in R.
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.
erilu.github.io
Modified the square.github.io website to turn it into a data analysis portfolio.
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.
mode-sql-tutorial-notes
Notes from my walkthrough of the SQL tutorial by Mode, including solutions to their exercises