date_range 开始2016年4月15日
event_note 结束于2016年5月8日
list 4个序列
assignment 等级:入门
chat_bubble_outline 语言 : 英语
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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.

The courses in this series will be released sequentially each month 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.

HarvardX requires individuals who enroll in its courses on edX to abide by the terms of the edX honor code. HarvardX will take appropriate corrective action in response to violations of the edX honor code, which may include dismissal from the HarvardX course; revocation of any certificates received for the HarvardX course; or other remedies as circumstances warrant. No refunds will be issued in the case of corrective action for such violations. Enrollees who are taking HarvardX courses as part of another program will also be governed by the academic policies of those programs.

HarvardX pursues the science of learning. By registering as an online learner in an HX course, you will also participate in research about learning. Read our research statement to learn more.

Harvard University and HarvardX are committed to maintaining a safe and healthy educational and work environment in which no member of the community is excluded from participation in, denied the benefits of, or subjected to discrimination or harassment in our program. All members of the HarvardX community are expected to abide by Harvard policies on nondiscrimination, including sexual harassment, and the edX Terms of Service. If you have any questions or concerns, please contact harvardx@harvard.edu and/or report your experience through the edX contact form.

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课程大纲

  • Mapping reads
  • Quality assessment of Next Generation Data
  • Analyzing RNA-seq data
  • Analyzing DNA methylation data
  • Analyzing ChIP Seq data
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教师

  • Rafael Irizarry
  • Michael Love
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Harvard Université

L’université Harvard (Harvard University), ou plus simplement Harvard, est une université privée américaine située à Cambridge, ville de l'agglomération de Boston, dans le Massachusetts. Fondée le 28 octobre 1636, c'est le plus ancien établissement d'enseignement supérieur des États-Unis.

Elle fait partie de l'Ivy League, regroupement informel des huit universités de la côte Est des États-Unis. Plus de 70 de ses étudiants ont reçu un prix Nobel. Le corps enseignant est constitué de 2 497 professeurs, pour 6 715 étudiants de premier cycle (undergraduate, en anglais) et 12 424 étudiants de cycle supérieur (graduate en anglais). Harvard attire des étudiants du monde entier (132 nationalités représentées en 2004).

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Edx

EdX est une plateforme d'apprentissage en ligne (dite FLOT ou MOOC). Elle héberge et met gratuitement à disposition des cours en ligne de niveau universitaire à travers le monde entier. Elle mène également des recherches sur l'apprentissage en ligne et la façon dont les utilisateurs utilisent celle-ci. Elle est à but non lucratif et la plateforme utilise un logiciel open source.

EdX a été fondée par le Massachusetts Institute of Technology et par l'université Harvard en mai 2012. En 2014, environ 50 écoles, associations et organisations internationales offrent ou projettent d'offrir des cours sur EdX. En juillet 2014, elle avait plus de 2,5 millions d'utilisateurs suivant plus de 200 cours en ligne.

Les deux universités américaines qui financent la plateforme ont investi 60 millions USD dans son développement. La plateforme France Université Numérique utilise la technologie openedX, supportée par Google.

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