Lecture

Introduction to R Programming for Genetics & Genomics

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In course

BIO-373: Genetics and genomics

The theoretical part of this course covers classical genetics and contemporary genomics. Because bioinformatics has become important for genomic research, the course also includes practical applications to genomic analyses using Python, including group pro ...

Description

This lecture provides a global introduction to a course on Genetics and Genomics, with a focus on the R programming language. The instructor introduces the course structure, followed by a lecture on R syntax and programming by Vincent Gardeux, merged with an interactive exercise session. The course covers topics such as genes, chromosomes, heredity, understanding the genome, and practical applications with R. Reference books and resources for interactive questions are also provided.

Instructors (2)

Bart Deplancke

Bart Deplancke graduated as a Biochemical Engineer at Ghent University (Belgium, 1998) after which he pursued doctoral studies in Immunobiology at the University of Illinois (USA) and postdoctoral work in regulatory genomics at the Harvard and UMass Medical Schools (USA). In 2007, he established his lab at the EPFL School of Life Sciences where he is now a Full Professor and former Vice-Dean of Innovation. There, he is developing new, often single cell-related technologies to study how the genome mediates c

Jacques Fellay

Jacques Fellay is a medical scientist with expertise in infectious diseases and human genomics. He obtained his MD from the University of Lausanne in 2002 and his PhD from University of Utrecht. After a clinical training in infectious diseases in Switzerland and a 4-years postdoctoral fellowship at Duke University, he joined the EPFL in April 2011 with an SNF Professorship. On top of his EPFL affiliation, Jacques is also Head of Precision Medicine at the University Hospital (CHUV) in Lausanne, Group Leader at the Swiss Institute of Bioinformatics, and Co-director of the Health2030 Genome Center at Campus Biotech in Geneva.

Official source

Ontological neighbourhood

Theoretical computer science

Programming language theory: High-level programming languages

Related concepts (32)

Y chromosome

The Y chromosome is one of two sex chromosomes in therian mammals and other organisms. The other sex chromosome is the X chromosome. Y is normally the sex-determining chromosome in many species, since it is the presence or absence of Y that determines the male or female sex of offspring produced in sexual reproduction. In mammals, the Y chromosome contains the gene SRY, which triggers male development. The DNA in the human Y chromosome is composed of about 62 million base pairs, making it similar in size to chromosome 19.

R (programming language)

R is a programming language for statistical computing and graphics supported by the R Core Team and the R Foundation for Statistical Computing. Created by statisticians Ross Ihaka and Robert Gentleman, R is used among data miners, bioinformaticians and statisticians for data analysis and developing statistical software. The core R language is augmented by a large number of extension packages containing reusable code and documentation. According to user surveys and studies of scholarly literature databases, R is one of the most commonly used programming languages in data mining.

X chromosome

The X chromosome is one of the two sex chromosomes in many organisms, including mammals, and is found in both males and females. It is a part of the XY sex-determination system and XO sex-determination system. The X chromosome was named for its unique properties by early researchers, which resulted in the naming of its counterpart Y chromosome, for the next letter in the alphabet, following its subsequent discovery. It was first noted that the X chromosome was special in 1890 by Hermann Henking in Leipzig.

Data warehouse

In computing, a data warehouse (DW or DWH), also known as an enterprise data warehouse (EDW), is a system used for reporting and data analysis and is considered a core component of business intelligence. Data warehouses are central repositories of integrated data from one or more disparate sources. They store current and historical data in one single place that are used for creating analytical reports for workers throughout the enterprise. This is beneficial for companies as it enables them to interrogate and draw insights from their data and make decisions.

Data management

Data management comprises all disciplines related to handling data as a valuable resource. The concept of data management arose in the 1980s as technology moved from sequential processing (first punched cards, then magnetic tape) to random access storage. Since it was now possible to store a discrete fact and quickly access it using random access disk technology, those suggesting that data management was more important than business process management used arguments such as "a customer's home address is stored in 75 (or some other large number) places in our computer systems.

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