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Case Studies in Functional Genomics

Harvard University via edX

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  • Provider edX
  • Subject Data Science
  • $ Cost Free Online Course
  • Session Self Paced
  • Language English
  • Certificate $49 Certificate Available
  • Effort 2-4 hours a week
  • Start Date
  • Duration 4 weeks long

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Overview

We will explain how to start with raw data, and perform the standard processing and normalization steps to get to the point where one can investigate relevant biological questions. Throughout the case studies, we will make use of exploratory plots to get a general overview of the shape of the data and the result of the experiment. We start with RNA-seq data analysis covering basic concepts of RNA-seq and a first look at FASTQ files. We will also go over quality control of FASTQ files; aligning RNA-seq reads; visualizing alignments and move on to analyzing RNA-seq at the gene-level: counting reads in genes; Exploratory Data Analysis and variance stabilization for counts; count-based differential expression; normalization and batch effects. Finally, we cover RNA-seq at the transcript-level: inferring expression of transcripts (i.e. alternative isoforms); differential exon usage. We will learn the basic steps in analyzing DNA methylation data, including reading the raw data, normalization, and finding regions of differential methylation across multiple samples. The course will end with a brief description of the basic steps for analyzing ChIP-seq datasets, from read alignment, to peak calling, and assessing differential binding patterns across multiple samples.

Given the diversity in educational background of our students we have divided the series into seven parts. You can take the entire series or individual courses that interest you. If you are a statistician you should consider skipping the first two or three courses, similarly, if you are biologists you should consider skipping some of the introductory biology lectures. Note that the statistics and programming aspects of the class ramp up in difficulty relatively quickly across the first three courses. By the third course will be teaching advanced statistical concepts such as hierarchical models and by the fourth advanced software engineering skills, such as parallel computing and reproducible research concepts.

These courses make up 2 XSeries and are self-paced:

PH525.1x: Statistics and R for the Life Sciences

PH525.2x: Introduction to Linear Models and Matrix Algebra

PH525.3x: Statistical Inference and Modeling for High-throughput Experiments

PH525.4x: High-Dimensional Data Analysis

PH525.5x: Introduction to Bioconductor: annotation and analysis of genomes and genomic assays

PH525.6x: High-performance computing for reproducible genomics

PH525.7x: Case studies in functional genomics


This class was supported in part by NIH grant R25GM114818.

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Taught by

Michael Love and Rafael Irizarry

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Review for edX's Case Studies in Functional Genomics
3.0 Based on 1 reviews

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Brandt P
3.0 2 years ago
by Brandt completed this course, spending 3 hours a week on it and found the course difficulty to be medium.
(Note I took these prior to their reorganization/combination. Back then they were 4 one-week courses, of which I took three, so I will review those modules below and assume that the material in the new course is similar).

>>>>RNA-seq:

This is the first case study course and 5th overall course in the PH525 sequence offered by HarvardX through EdX. I had high hopes for these case studies going in, but I left somewhat disappointed. I had hoped to learn how to work through an entire genomics pipeline, but instead most of the questions were similar to those in the Intro t…
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