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advancedinformatics2021

Course materials for 2021

advancedinformatics_rmarkdown_week2

R markdown work for Advanced Informatics Winter 2021

advancedinformatics_rmarkdown_week3

R markdown exercise for week 3

advancedinformatics_week4

Week 4 snakemake exercise

advancedinformatics_week4_snakemake

Week 4 snakemake exercises

advancedinformatics_week5_plotting

Week 5 plotting in R and Python.

advancedinformatics_week6-10_pipelines

Week 6-10 with Dr. Long, running pipelines for DNA-seq, ATAC-seq, and RNA-seq.

advancedinformaticsexercises

bulk_atac_pipeline

Pipeline adapted from Klebea Carvalho and Dr. Rabi Murad from the Mortazavi lab, for remote server w/ SLURM scheduler.

c2c12_trackhub

ee282

enc4_mouse

Scripts to import ENCODE processed data for snRNA-seq experiments and snATAC-seq experiments to Seurat and ArchR objects, respectively.

enc4_mouse_paper

Code for the ENCODE4 single-nucleus mouse analysis.

lab_pipelines

Pipelines for analyzing data for different protocols in the Mortazavi lab

mirna_pipeline

Code for processing microRNA-seq data from fastq

ta-github

UCI COSMOS 2023 Cluster 6

wgcna

Consensus WGCNA and post-analysis between Downs syndrome microarray data in from GSE59630, Alzheimer's RNA seq data from Mayo Clinic, and Alzheimer's microarray data from Zhang lab.