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BF528 - Applications in Translational Bioinformatics
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Table of contents
BF528 - Applications in Translational Bioinformatics
Guides
Computational Environments Guide
Guide for requesting appropriate computational resources on the SCC
Project 0
Week 1: Genome Analytics
Week 2: Genome Analytics
Week 3: Genome Analytics
Week 4: Genome Analytics
Project 1
Week 1: RNAseq
Week 2: RNAseq
Week 3: RNAseq
Week 4: RNAseq
Project 2
Week 1: ChIPseq
Week 2: ChIPseq
Week 3: ChIPseq
Week 4: ChIPseq
Final Project
Final Project - single cell RNAseq
Lectures
Introduction
Genomics, Genes, and Genomes
git
Computational Pipeline Strategies
Computational Environment Management
Sequence Analysis Fundamentals
2nd Gen Sequencing
Sequence Analysis - RNA-Seq 1
Sequence Analysis - RNA-Seq 2
SCC cluster usage
Biological Data Formats
Gene sets and enrichment
Replicability vs Reproducibility Strategies
Putting it all together - snakemake
Sequence Analysis - ChIP-Seq
Genome Browsers
Sequence Analysis - ATAC-Seq
Project 2 - Week 1 Check-in
Biological Databases
Genomic Variation and SNP Analysis
Microbiome: Metagenomics
Microbiome: 16S
Proteomics
Metabolomics
Docker
Single Cell Analysis Part 1
Single Cell Analysis Part 2
Single Cell Analysis Part 3
Spatial Transcriptomics
Week 3: ChIPseq
0.12
Download HG38 gene BED from UCSC table browser
0.13
ComputeMatrix for IP samples
0.14
Plotprofile for IP samples
0.15
Annotate peaks
0.16
FindMotifs
Week 2: ChIPseq
Week 4: ChIPseq
On this page
Week 3: ChIPseq
0.12
Download HG38 gene BED from UCSC table browser
0.13
ComputeMatrix for IP samples
0.14
Plotprofile for IP samples
0.15
Annotate peaks
0.16
FindMotifs