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BF528 - Applications in Translational Bioinformatics
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Table of contents
BF528 - Applications in Translational Bioinformatics
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
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Assignment 0: snakemake
Project Writeup Instructions
Project 1: Transcriptional Profile of Mammalian Cardiac Regeneration with mRNA-Seq
Week 1: RNAseq
Week 2: RNAseq
Week 3: RNAseq
Week 4: RNAseq
Week 5: RNAseq
Project 2: ChIPseq analysis of the human transcription factor Runx1
Week 1: ChIPseq
Week 2: ChIPseq
Week 3: ChIPseq
Week 4: ChIPseq
Week 5: ChIPseq
Project 3: Individual Project
Project 3: RNAseq Individual Project
Project 3: ChIPseq Individual Project
Project 3: ATACseq Individual Project
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Single Cell Analysis Part 3
Assignment 0: snakemake
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